scholarly journals Acyltransferases as Tools for Polyketide Synthase Engineering

Antibiotics ◽  
2018 ◽  
Vol 7 (3) ◽  
pp. 62 ◽  
Author(s):  
Ewa Musiol-Kroll ◽  
Wolfgang Wohlleben
Keyword(s):  
Natural Products ◽  
Rational Design ◽  
Polyketide Synthase ◽  
Antifungal Agents ◽  
Relevant Literature ◽  
Structural Diversity ◽  
Building Blocks ◽  
Assembly Lines ◽  
Acyl Carrier Proteins ◽  
Polyketide Biosynthesis

Polyketides belong to the most valuable natural products, including diverse bioactive compounds, such as antibiotics, anticancer drugs, antifungal agents, immunosuppressants and others. Their structures are assembled by polyketide synthases (PKSs). Modular PKSs are composed of modules, which involve sets of domains catalysing the stepwise polyketide biosynthesis. The acyltransferase (AT) domains and their “partners”, the acyl carrier proteins (ACPs), thereby play an essential role. The AT loads the building blocks onto the “substrate acceptor”, the ACP. Thus, the AT dictates which building blocks are incorporated into the polyketide structure. The precursor- and occasionally the ACP-specificity of the ATs differ across the polyketide pathways and therefore, the ATs contribute to the structural diversity within this group of complex natural products. Those features make the AT enzymes one of the most promising tools for manipulation of polyketide assembly lines and generation of new polyketide compounds. However, the AT-based PKS engineering is still not straightforward and thus, rational design of functional PKSs requires detailed understanding of the complex machineries. This review summarizes the attempts of PKS engineering by exploiting the AT attributes for the modification of polyketide structures. The article includes 253 references and covers the most relevant literature published until May 2018.

scholarly journals Engineered chimeras unveil swappable modular features of fatty acid and polyketide synthase acyl carrier proteins

2021 ◽  
Author(s):  
Yae In Cho ◽  
Claire L Armstrong ◽  
Ariana Sulpizio ◽  
Kofi K Acheampong ◽  
Kameron N Banks ◽  
...  
Keyword(s):  
Natural Products ◽  
Fatty Acid ◽  
Fatty Acid Synthase ◽  
Polyketide Synthase ◽  
Building Blocks ◽  
Combinatorial Biosynthesis ◽  
Biosynthetic Pathways ◽  
Carrier Proteins ◽  
Acyl Carrier Proteins ◽  
E Coli

The strategic redesign of microbial biosynthetic pathways is a compelling route to access molecules of diverse structure and function in a potentially environmentally sustainable fashion. The promise of this approach hinges on an improved understanding of acyl carrier proteins (ACPs), which serve as central hubs in biosynthetic pathways. These small, flexible proteins mediate the transport of molecular building blocks and intermediates to enzymatic partners that extend and tailor the growing natural products. Past combinatorial biosynthesis efforts have failed due to incompatible ACP-enzyme pairings. Herein we report the design of chimeric ACPs with features of the actinorhodin polyketide synthase ACP (ACT) and of the E. coli fatty acid synthase (FAS) ACP (AcpP). We evaluate the ability of the chimeric ACPs to interact with the E. coli FAS ketosynthase FabF, which represents an interaction essential to building the carbon backbone of the synthase molecular output. Given that AcpP interacts with FabF but ACT does not, we sought to exchange modular features of ACT with AcpP to confer functionality with FabF. The interactions of chimeric ACPs with FabF were interrogated using sedimentation velocity experiments, surface plasmon resonance analyses, mechanism-based crosslinking assays, and molecular dynamics simulations. Results suggest that the residues guiding AcpP-FabF compatibility and ACT-FabF incompatibility may reside in the loop I, α-helix II region. These findings can inform the development of strategic secondary element swaps that expand the enzyme compatibility of ACPs across systems and therefore represent a critical step towards the strategic engineering of unnatural natural products.

Secondary metabolites, their structural diversity, bioactivity, and ecological functions: An overview

2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Berhanu M. Abegaz ◽  
Henok H. Kinfe
Keyword(s):  
Natural Products ◽  
Secondary Metabolites ◽  
Structural Diversity ◽  
Building Blocks ◽  
Narrative Texts ◽  
Ecological Functions ◽  
Acetyl Coenzyme A ◽  
Primary Metabolites ◽  
Geranyl Diphosphate ◽  
Aromatic Polyketides

Abstract Natural products are also called secondary metabolites to distinguish them from the primary metabolites, i.e. those natural compounds like glucose, amino acids, etc. that are present in every living cell and are used and required in the essential life processes of cells. Natural products are classified according to their metabolic building blocks into alkaloids, fatty acids, polyketides, phenyl propanoids and aromatic polyketides, and terpenoids. The structural diversity of natural products is explored using the scaffold approach focusing on the characteristic carbon frameworks.  Aside from discussing specific alkaloids that are either pharmacologically (e.g. boldine, berberine, galantamine, etc.) or historically (caffeine, atropine, lobeline, etc.) important alkaloids, a single chart is presented which shows the typical scaffolds of the most important subclasses of alkaloids.  How certain classes of natural products are formed in nature from simple biochemical ‘building blocks’ are shown using graphical schemes. This has been done for a typical tetra-ketide (6-methylsalicylic acid) from acetyl coenzyme A, or in general to all the major subclasses of terpenes.   An important aspect of understanding the structural diversity of natural products is to recognize how some compounds can be visualized as key intermediates for enzyme mediated transformation to several other related structures.  This is seen in the case of how arachidonic acid can transform into prostaglandins, or geranyl diphosphate to various monoterpenes, or squalene epoxide to various pentacyclic triterpenes, or cholesterol transforming to sex hormones, bile acids and the cardioactive cardenolides and bufadienolides. These are presented in carefully designed schemes and charts that are appropriately placed in the relevant sections of the narrative texts.  The ecological functions and pharmacological properties of natural products are also presented showing wherever possible how the chemical scaffolds have led to developing drugs as well as commercial products like sweeteners.

Natural polyenic macrolactams and polycyclic derivatives generated by transannular pericyclic reactions: optimized biogenesis challenging chemical synthesis

2021 ◽  
Author(s):  
Rosana Alvarez ◽  
Angel R. de Lera
Keyword(s):  
Natural Products ◽  
Chemical Synthesis ◽  
Polyketide Synthase ◽  
Pericyclic Reactions ◽  
Large Collection ◽  
Assembly Lines ◽  
Nonribosomal Peptide

Genetically-encoded polyenic macrolactams, which are constructed by Nature using hybrid polyketide synthase/nonribosomal peptide synthase (PKSs/NRPSs) assembly lines, are part of the large collection of natural products isolated from bacteria.

scholarly journals Expanding the Fluorine Chemistry of Living Systems Using Engineered Polyketide Synthase Pathways

Science ◽  
2013 ◽  
Vol 341 (6150) ◽  
pp. 1089-1094 ◽  
Author(s):  
Mark C. Walker ◽  
Benjamin W. Thuronyi ◽  
Louise K. Charkoudian ◽  
Brian Lowry ◽  
Chaitan Khosla ◽  
...  
Keyword(s):  
Natural Products ◽  
Synthetic Biology ◽  
Natural Product ◽  
Polyketide Synthase ◽  
Building Blocks ◽  
Living Systems ◽  
Synthetic Compounds ◽  
Fluorinated Building Blocks

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.

scholarly journals Discovery of the leinamycin family of natural products by mining actinobacterial genomes

2017 ◽  
Vol 114 (52) ◽  
pp. E11131-E11140 ◽  
Author(s):  
Guohui Pan ◽  
Zhengren Xu ◽  
Zhikai Guo ◽  
Hindra ◽  
Ming Ma ◽  
...  
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Structural Diversity ◽  
Building Blocks ◽  
Combinatorial Biosynthesis ◽  
Pathway Engineering ◽  
Natural Product Discovery ◽  
Knowledge Based ◽  
Metabolic Pathway Engineering ◽  
Strain Collection

Nature’s ability to generate diverse natural products from simple building blocks has inspired combinatorial biosynthesis. The knowledge-based approach to combinatorial biosynthesis has allowed the production of designer analogs by rational metabolic pathway engineering. While successful, structural alterations are limited, with designer analogs often produced in compromised titers. The discovery-based approach to combinatorial biosynthesis complements the knowledge-based approach by exploring the vast combinatorial biosynthesis repertoire found in Nature. Here we showcase the discovery-based approach to combinatorial biosynthesis by targeting the domain of unknown function and cysteine lyase domain (DUF–SH) didomain, specific for sulfur incorporation from the leinamycin (LNM) biosynthetic machinery, to discover the LNM family of natural products. By mining bacterial genomes from public databases and the actinomycetes strain collection at The Scripps Research Institute, we discovered 49 potential producers that could be grouped into 18 distinct clades based on phylogenetic analysis of the DUF–SH didomains. Further analysis of the representative genomes from each of the clades identified 28 lnm-type gene clusters. Structural diversities encoded by the LNM-type biosynthetic machineries were predicted based on bioinformatics and confirmed by in vitro characterization of selected adenylation proteins and isolation and structural elucidation of the guangnanmycins and weishanmycins. These findings demonstrate the power of the discovery-based approach to combinatorial biosynthesis for natural product discovery and structural diversity and highlight Nature’s rich biosynthetic repertoire. Comparative analysis of the LNM-type biosynthetic machineries provides outstanding opportunities to dissect Nature’s biosynthetic strategies and apply these findings to combinatorial biosynthesis for natural product discovery and structural diversity.

scholarly journals Recent advances in the biosynthesis of unusual polyketide synthase substrates

2016 ◽  
Vol 33 (2) ◽  
pp. 150-161 ◽  
Author(s):  
Lauren Ray ◽  
Bradley S. Moore
Keyword(s):  
Natural Products ◽  
Polyketide Synthase ◽  
Building Blocks ◽  
Pharmacological Activities ◽  
Chemical Complexity ◽  
Recent Advances ◽  
Biological And Pharmacological Activities

Polyketides comprise a diverse class of natural products, with many important biological and pharmacological activities. Substrates functioning as starter units and extender units during their assembly significantly contribute to the chemical complexity exhibited by this class of natural products. This highlight provides an overview of the recent advances in understanding the diversity of these polyketide synthase (PKS) building blocks.

scholarly journals Thiocysteine lyases as polyketide synthase domains installing hydropersulfide into natural products and a hydropersulfide methyltransferase

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Song Meng ◽  
Andrew D. Steele ◽  
Wei Yan ◽  
Guohui Pan ◽  
Edward Kalkreuter ◽  
...  
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Assembly Line ◽  
Polyketide Synthase ◽  
Genome Mining ◽  
Assembly Lines ◽  
Biologically Relevant ◽  
Peptide Synthetase ◽  
Adenosyl Methionine

AbstractNature forms S-S bonds by oxidizing two sulfhydryl groups, and no enzyme installing an intact hydropersulfide (-SSH) group into a natural product has been identified to date. The leinamycin (LNM) family of natural products features intact S-S bonds, and previously we reported an SH domain (LnmJ-SH) within the LNM hybrid nonribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) assembly line as a cysteine lyase that plays a role in sulfur incorporation. Here we report the characterization of an S-adenosyl methionine (SAM)-dependent hydropersulfide methyltransferase (GnmP) for guangnanmycin (GNM) biosynthesis, discovery of hydropersulfides as the nascent products of the GNM and LNM hybrid NRPS-PKS assembly lines, and revelation of three SH domains (GnmT-SH, LnmJ-SH, and WsmR-SH) within the GNM, LNM, and weishanmycin (WSM) hybrid NRPS-PKS assembly lines as thiocysteine lyases. Based on these findings, we propose a biosynthetic model for the LNM family of natural products, featuring thiocysteine lyases as PKS domains that directly install a -SSH group into the GNM, LNM, or WSM polyketide scaffold. Genome mining reveals that SH domains are widespread in Nature, extending beyond the LNM family of natural products. The SH domains could also be leveraged as biocatalysts to install an -SSH group into other biologically relevant scaffolds.

scholarly journals Engineering the acyltransferase substrate specificity of assembly line polyketide synthases

2013 ◽  
Vol 10 (85) ◽  
pp. 20130297 ◽  
Author(s):  
Briana J. Dunn ◽  
Chaitan Khosla
Keyword(s):  
Natural Products ◽  
Substrate Specificity ◽  
Assembly Line ◽  
Current Knowledge ◽  
Structural Diversity ◽  
Structural Data ◽  
Building Blocks ◽  
Polyketide Synthases ◽  
Biologically Active ◽  
Recent Developments

Polyketide natural products act as a broad range of therapeutics, including antibiotics, immunosuppressants and anti-cancer agents. This therapeutic diversity stems from the structural diversity of these small molecules, many of which are produced in an assembly line manner by modular polyketide synthases. The acyltransferase (AT) domains of these megasynthases are responsible for selection and incorporation of simple monomeric building blocks, and are thus responsible for a large amount of the resulting polyketide structural diversity. The substrate specificity of these domains is often targeted for engineering in the generation of novel, therapeutically active natural products. This review outlines recent developments that can be used in the successful engineering of these domains, including AT sequence and structural data, mechanistic insights and the production of a diverse pool of extender units. It also provides an overview of previous AT domain engineering attempts, and concludes with proposed engineering approaches that take advantage of current knowledge. These approaches may lead to successful production of biologically active ‘unnatural’ natural products.

Formation of Carbon-Oxygen Bond Mediated by Hypervalent Iodine Reagents Under Metal-free Conditions

2020 ◽  
Vol 17 ◽  
Author(s):  
Ayesha Jalil ◽  
Yaxin O Yang ◽  
Zhendong Chen ◽  
Rongxuan Jia ◽  
Tianhao Bi ◽  
...  
Keyword(s):  
Natural Products ◽  
Bond Formation ◽  
Building Blocks ◽  
Review Article ◽  
Hypervalent Iodine ◽  
Metal Free ◽  
Bioactive Natural Products ◽  
The Past ◽  
Oxygen Bond ◽  
Privileged Scaffolds

: Hypervalent iodine reagents are a class of non-metallic oxidants have been widely used in the construction of several sorts of bond formations. This surging interest in hypervalent iodine reagents is essentially due to their very useful oxidizing properties, combined with their benign environmental character and commercial availability from the past few decades ago. Furthermore, these hypervalent iodine reagents have been used in the construction of many significant building blocks and privileged scaffolds of bioactive natural products. The purpose of writing this review article is to explore all the transformations in which carbon-oxygen bond formation occurred by using hypervalent iodine reagents under metal-free conditions

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