Bioinformatic prediction of the stereoselectivity of modular polyketide synthase: an update of the sequence motifs in ketoreductase domain

• Changjun Xiang,
• Shunyu Yao,
• Ruoyu Wang and
• Lihan Zhang

Beilstein J. Org. Chem. 2024, 20, 1476–1485, doi:10.3762/bjoc.20.131

• : bioinformatics; conserved motifs; ketoreductase; polyketide synthase; stereocontrol; Introduction Type I modular polyketide synthases (PKSs) are large enzyme complexes that play a crucial role in the biosynthesis of bacterial polyketides, including many important clinical drugs such as erythromycin (antibiotic

Cofactor-independent C–C bond cleavage reactions catalyzed by the AlpJ family of oxygenases in atypical angucycline biosynthesis

• Jinmin Gao,
• Liyuan Li,
• Shijie Shen,
• Guomin Ai,
• Bin Wang,
• Fang Guo,
• Tongjian Yang,
• Hui Han,
• Zhengren Xu,
• Guohui Pan and
• Keqiang Fan

Beilstein J. Org. Chem. 2024, 20, 1198–1206, doi:10.3762/bjoc.20.102

• cofactor-independent manner. Keywords: angucyclines; aromatic polyketide; biosynthesis; cofactor-independent oxygenase; oxidative rearrangement reaction; Introduction The angucyclines represent a large class of natural products biosynthesized by type II polyketide synthases. Within this category, a

Activity assays of NnlA homologs suggest the natural product N-nitroglycine is degraded by diverse bacteria

• Kara A. Strickland,
• Brenda Martinez Rodriguez,
• Ashley A. Holland,
• Shelby Wagner,
• Michelle Luna-Alva,
• David E. Graham and
• Jonathan D. Caranto

Beilstein J. Org. Chem. 2024, 20, 830–840, doi:10.3762/bjoc.20.75

• . NNG is a non-proteinogenic amino acid, similar to other such N–N containing compounds such as piperazic acid and hydrazinoacetic acid [43]. These precursors are incorporated into larger NPs by non-ribosomal peptide synthases or polyketide synthases, and NNG may have a similar fate [44][45]. Another

Substrate specificity of a ketosynthase domain involved in bacillaene biosynthesis

• Zhiyong Yin and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2024, 20, 734–740, doi:10.3762/bjoc.20.67

• glutamate decarboxylase, and incubated with BaeJ-KS2. Substrate binding was demonstrated through 13C NMR analysis of the products against the background of various control experiments. Keywords: bacillaene; biosynthesis; enzyme mechanisms; isotopes; trans-AT polyketide synthases; Introduction Polyketides

• are a large class of natural products which often exhibit potent biological activities for their application in medicine, e.g., as antibiotics or immunosuppressants [1]. Despite their high structural variability all compounds from this class are commonly made through the action of polyketide synthases

• only for the incorporation of one extender unit [2][3]. Although enzyme domains with various specialised catalytic functions can be found as integral part of polyketide synthases, three domain types are fundamental to their biosynthesis, resembling the same logic as observed for fatty acid biosynthesis

Chemoenzymatic synthesis of macrocyclic peptides and polyketides via thioesterase-catalyzed macrocyclization

• Senze Qiao,
• Zhongyu Cheng and
• Fuzhuo Li

Beilstein J. Org. Chem. 2024, 20, 721–733, doi:10.3762/bjoc.20.66

• and multifunctional enzymatic assembly, nonribosomal peptide synthases (NRPS), polyketide synthases (PKS), and hybrid NRPS/PKS systems, which are organized into sets of functional domains known as modules and function through a similar mechanism [9][10][11][12]. Each NRPS module is composed of three

• terminal polyketide synthases (PKSs) in juvenimicin biosynthesis in 2017 [75], which presented a chance to accomplish the chemoenzymatic total syntheses of tylactone and the juvenimicins (Scheme 7). To generate an appropriately activated tylactone hexaketide intermediate 49, two key fragments, aldehyde 42

Navigating and expanding the roadmap of natural product genome mining tools

• Friederike Biermann,
• Sebastian L. Wenski and
• Eric J. N. Helfrich

Beilstein J. Org. Chem. 2022, 18, 1656–1671, doi:10.3762/bjoc.18.178

• -like pathways are canonical type I cis-acyltransferase polyketide synthases (PKSs) and type A non-ribosomal peptide synthetases (NRPSs) (Figure 2A) [25][26]. The substrate specificity of the specificity conferring domains in each module can be predicted from the sequences of adenylation (A) (for NRPS

Bioinspired tetraamino-bisthiourea chiral macrocycles in catalyzing decarboxylative Mannich reactions

• Hao Guo,
• Yu-Fei Ao,
• De-Xian Wang and
• Qi-Qiang Wang

Beilstein J. Org. Chem. 2022, 18, 486–496, doi:10.3762/bjoc.18.51

• cavity could resemble the circumstance of the catalytic triad of Polyketide synthases (PKSs) [40][41][42] (Figure 1). On the other hand, the organocatalytic asymmetric decarboxylative addition reactions of MAHTs to imines provide an efficient means for accessing valuable chiral β-amino esters [43][44][45

Fabclavine diversity in Xenorhabdus bacteria

• Sebastian L. Wenski,
• Harun Cimen,
• Natalie Berghaus,
• Sebastian W. Fuchs,
• Selcuk Hazir and
• Helge B. Bode

Beilstein J. Org. Chem. 2020, 16, 956–965, doi:10.3762/bjoc.16.84

• ), and polyketide synthases (PKS). Selected Xenorhabdus and Photorhabdus mutant strains were generated applying a chemically inducible promoter in front of the suggested fabclavine (fcl) biosynthesis gene cluster (BGC), followed by the analysis of the occurring fabclavines. Subsequently, known and

Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering

• Eric J. N. Helfrich,
• Geng-Min Lin,
• Christopher A. Voigt and
• Jon Clardy

Beilstein J. Org. Chem. 2019, 15, 2889–2906, doi:10.3762/bjoc.15.283

• thiotemplated assembly lines, such as type I polyketide synthases (PKS) and nonribosomal peptide synthetases (NRPS), are modular, with each module contributing a distinct fragment to the final product’s core structure – a short-chain carboxylic acid (PKS) or an amino acid (NRPS). The modularly defined template

• thiotemplate biosynthetic pathways that enable relatively precise predictions of natural product core structures (e.g., the colinearity rule in NRPSs and cis-acyltransferase polyketide synthases [8]), no such rules exist for the predictions of the cyclic hydrocarbon backbone produced by TCs [1]. This is likely

Sulfation and amidinohydrolysis in the biosynthesis of giant linear polyenes

• Hui Hong,
• Markiyan Samborskyy,
• Katsiaryna Usachova,
• Katharina Schnatz and
• Peter F. Leadlay

Beilstein J. Org. Chem. 2017, 13, 2408–2415, doi:10.3762/bjoc.13.238

• Bacterial modular polyketide synthases (PKSs) follow an assembly-line paradigm for enzyme catalysis, in which each round of chain extension requires a different set, or module, of enzymatic activities [1][2][3][4]. Among the more remarkable natural products derived by this pathway is the giant linear

Strategies in megasynthase engineering – fatty acid synthases (FAS) as model proteins

• Manuel Fischer and
• Martin Grininger

Beilstein J. Org. Chem. 2017, 13, 1204–1211, doi:10.3762/bjoc.13.119

• Megasynthases are large multienzyme proteins that produce a plethora of important natural compounds by catalyzing the successive condensation and modification of precursor units. Within the class of megasynthases, polyketide synthases (PKS) are responsible for the production of a large spectrum of bioactive

• engineering strategies in the light of the newly emerging structural information on megasynthases, and argue that fatty acid synthases (FAS) are and will be valuable objects for further developing this field. Keywords: fatty acid synthases; megasynthases; metabolic enzyme engineering; polyketide synthases

• antineoplastic doxorubicin and by the antiparasitic avermectin (Figure 1a) [1]. PK are assembled from acyl-coenzyme A (acyl-CoA) units via a series of Claisen-type condensation reactions catalyzed by polyketide synthases (PKS) (Figure 1b). PKS occur as large multifunctional enzymes, termed megasynthases, which

Polyketide stereocontrol: a study in chemical biology

• Kira J. Weissman

Beilstein J. Org. Chem. 2017, 13, 348–371, doi:10.3762/bjoc.13.39

• biosynthesis of reduced polyketides in bacteria by modular polyketide synthases (PKSs) proceeds with exquisite stereocontrol. As the stereochemistry is intimately linked to the strong bioactivity of these molecules, the origins of stereochemical control are of significant interest in attempts to create

• this approach to provide answers to fundamental biological questions. Keywords: chemical biology; polyketide synthases; reduced polyketides; stereocontrol; Introduction Reduced polyketides and their derivatives form the basis for a number of medicines in current clinical usage, notably anti

• product structures by gas-chromatography/mass spectrometry (GC–MS) and liquid chromatography (LC)–MS. Review Biosynthesis of complex polyketides by modular PKSs and stereochemical considerations The reduced or complex class of polyketides is assembled in bacteria by gigantic multienzymes called polyketide

Evidence for an iterative module in chain elongation on the azalomycin polyketide synthase

• Hui Hong,
• Yuhui Sun,
• Yongjun Zhou,
• Emily Stephens,
• Markiyan Samborskyy and
• Peter F. Leadlay

Beilstein J. Org. Chem. 2016, 12, 2164–2172, doi:10.3762/bjoc.12.206

• ; marginolactone; natural products; polyketide synthase; Introduction Bacterial modular Type I polyketide synthases (PKSs) are multienzymes that govern the biosynthesis of diverse complex polyketide natural products, including clinically useful antibiotics, immunosuppressants, and antitumor compounds. They follow

• ) animal fatty acid synthases and that on bacterial modular polyketide synthases, and it also hints at what could be a major mechanism for the evolution of these processive systems. Nevertheless, the highly repetitive nature of the genes encoding modular PKS makes it easy to misassemble sequence data, and

Biosynthesis of oxygen and nitrogen-containing heterocycles in polyketides

• Franziska Hemmerling and
• Frank Hahn

Beilstein J. Org. Chem. 2016, 12, 1512–1550, doi:10.3762/bjoc.12.148

• ]. Polyketides Polyketide natural products are biosynthesised by polyketide synthases (PKSs) of the types I–III. Type I PKS are multimodular megaenzyme complexes that produce linear, reduced polyketides in an assembly line process that uses acyl carrier proteins (ACP), ketosynthase (KS) and acyl transferase (AT

Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides

• Andrew W. Truman

Beilstein J. Org. Chem. 2016, 12, 1250–1268, doi:10.3762/bjoc.12.120

• annotation software, which means that some putative RiPP precursors are not even listed in databases. Furthermore, novel classes are difficult to identify precisely due to their novelty compared to known pathways. This is in contrast to terpenes, polyketide synthases or NRPSs, whose pathways are all clearly

Recent highlights in biosynthesis research using stable isotopes

• Jan Rinkel and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2015, 11, 2493–2508, doi:10.3762/bjoc.11.271

• may not precisely follow the IUPAC rules. Review Polyketides Polyketide synthases (PKS) are multidomain enzymes that catalyze the formation of natural products via reaction steps similar to fatty acid biosynthesis, in which C2-units are fused in Claisen condensations and modified in an iterative or

• reductase [16], aflatoxin B1 (2) [17] and the potent antifungal agent amphotericin B (3) [18], which affects membrane integrity. The products of polyketide synthases (PKS) belong to the first secondary metabolites that were investigated using isotopically labeled compounds [19]. Feeding experiments using

A novel and widespread class of ketosynthase is responsible for the head-to-head condensation of two acyl moieties in bacterial pyrone biosynthesis

• Darko Kresovic,
• Florence Schempp,
• Zakaria Cheikh-Ali and
• Helge B. Bode

Beilstein J. Org. Chem. 2015, 11, 1412–1417, doi:10.3762/bjoc.11.152

• phosphopantetheinyl-transferase (PPtase) activity of NgrA [18]. Results and Discussion Usually pyrones are derived in a one-chain mechanism from type III polyketide synthases [2][19] rarely showing two alkyl substituents resulting from the incorporation of different extender units [20]. Contrary to this, experiments

Quantification of N-acetylcysteamine activated methylmalonate incorporation into polyketide biosynthesis

• Stephan Klopries,
• Uschi Sundermann and
• Frank Schulz

Beilstein J. Org. Chem. 2013, 9, 664–674, doi:10.3762/bjoc.9.75

• widespread application in current medicine and agriculture. Polyketide synthases (PKS), giant multienzyme complexes, play a pivotal role in their biosynthesis. PKS generate molecular complexity and diversity through a number of stepwise condensations in analogy to fatty acid synthases but with optional and

• here report the characterization of deuterated methylmalonyl-SNAC ester incorporation into polyketides in vivo and therefore in direct competition to endogenous MM-CoA, to determine the relative incorporation efficiency and the concentrations required to saturate polyketide synthases with the

• indeed competitive to coenzyme A in its ability to activate methylmalonate for utilization by polyketide synthases. Interestingly, the efficiency of incorporation is comparable between two rather different polyketide producers from two different bacterial genera, indicating a potentially more general

Unprecedented deoxygenation at C-7 of the ansamitocin core during mutasynthetic biotransformations

• Tobias Knobloch,
• Gerald Dräger,
• Wera Collisi,
• Florenz Sasse and
• Andreas Kirschning

Beilstein J. Org. Chem. 2012, 8, 861–869, doi:10.3762/bjoc.8.96

• ansamitocin producer [13][14][15][16][17], and Streptomyces hygroscopicus, the geldanamycin producer [18][19]. These engineered strains are unable to biosynthesize 3-amino-5-hydroxybenzoic acid (1) [20], the common starter unit for both polyketide synthases (PKS) (Scheme 1). These assembly-line-type

Natural product biosyntheses in cyanobacteria: A treasure trove of unique enzymes

• Jan-Christoph Kehr,
• Douglas Gatte Picchi and
• Elke Dittmann

Beilstein J. Org. Chem. 2011, 7, 1622–1635, doi:10.3762/bjoc.7.191

• combined with transport across the plasma membrane [12] (Figure 2). Macrolides in microorganisms are produced by modular type polyketide synthases (PKS) resembling NRPS with respect to their modular nature. In contrast to the peptide-synthesizing enzymes, different types of carboxylic acids are activated

• neurotoxins produced by cyanobacteria. A gene cluster for the alkaloid was first described for the strain Oscillatoria sp. PCC 6506 [36]. Analysis of the gene cluster and feeding studies suggested a biosynthetic scheme starting from L-proline and involving three polyketide synthases, with (S)-1-pyrolline-5

• cyanobacteria living in corraloid roots of Cycas circinalis. Schematic representation of enzymatic domains in A) nonribosomal peptide synthetases (NRPS); B) polyketide synthases (PKS) and C) the typical organisation of a ribosomal biosynthetic gene cluster. Abbreviations: C: Condensation domain; A: Adenylation