Chemical synthesis of tripeptide thioesters for the biotechnological incorporation into the myxobacterial secondary metabolite argyrin via mutasynthesis

• David C. B. Siebert,
• Roman Sommer,
• Domen Pogorevc,
• Michael Hoffmann,
• Silke C. Wenzel,
• Rolf Müller and
• Alexander Titz

Beilstein J. Org. Chem. 2019, 15, 2922–2929, doi:10.3762/bjoc.15.286

• synthetase (NRPS), mutasynthons often carry thioesters to mimic the natural phosphopantetheinyl conjugate [20]. For the argyrins, the Müller group identified the corresponding biosynthetic gene cluster from Cystobacter sp. SBCb004 [21], studied the biosynthesis (Figure 2) and established a heterologous

Nanangenines: drimane sesquiterpenoids as the dominant metabolite cohort of a novel Australian fungus, Aspergillus nanangensis

• Heather J. Lacey,
• Cameron L. M. Gilchrist,
• Andrew Crombie,
• John A. Kalaitzis,
• Daniel Vuong,
• Peter J. Rutledge,
• Peter Turner,
• John I. Pitt,
• Ernest Lacey,
• Yit-Heng Chooi and
• Andrew M. Piggott

Beilstein J. Org. Chem. 2019, 15, 2631–2643, doi:10.3762/bjoc.15.256

• bacteria, fungi, mammalian cells and plants. Bioinformatics analysis, including comparative analysis with other acyl drimenol-producing Aspergilli, led to the identification of a putative nanangenine biosynthetic gene cluster that corresponds to the proposed biosynthetic pathway for nanangenines. Keywords

• three human cell lines. None of the compounds tested showed any activity up to 100 μg mL−1 against the Gram-negative bacterium Escherichia coli (ATCC 25922), the fungus Candida albicans (ATCC 10231) or the plant Eragrostis tef (teff). Proposed biosynthesis and gene cluster The biosynthesis of drimane

• (Figure S52 in Supporting Information File 1). The analysis above, and the discovery of other homologous gene clusters in Aspergillus spp. that are known to produce acyl drimane sesquiterpenoids, support the identification of this as the putative biosynthetic gene cluster for nanangenines. Based on the

Current understanding and biotechnological application of the bacterial diterpene synthase CotB2

• Ronja Driller,
• Daniel Garbe,
• Norbert Mehlmer,
• Monika Fuchs,
• Keren Raz,
• Dan Thomas Major,
• Thomas Brück and
• Bernhard Loll

Beilstein J. Org. Chem. 2019, 15, 2355–2368, doi:10.3762/bjoc.15.228

• exclusively belong to class I TPSs. A few exceptions exist, for example the terpentedienyl-diphosphate synthase from Kitasatospora griseola [19], which belongs to class II, and PtmT1 from Streptomyces platensis in the platensimycin gene cluster [20], which is neither characteristic for class I nor class II

• cyclooctatin biosynthetic gene cluster in particular the TPS CotB2 from the soil bacterium Streptomyces melanosporofaciens MI614-43F2 (Figure 1) [31]. Cyclooctatin 5, with its distinct 5–8–5 ring motif, belongs to the fusicoccane diterpenoids that encompass a wide range of bioactivities, such as bacteriostatic

• industrial application. Within the subsequent paragraphs, we would like to summarize the current understanding of the unusual reaction mechanism and the biotechnological applications. Review The cyclooctatin biosynthetic gene cluster The cyclooctatin gene cluster from the soil bacterium S. melanosporofaciens

Bipolenins K–N: New sesquiterpenoids from the fungal plant pathogen Bipolaris sorokiniana

• Chin-Soon Phan,
• Hang Li,
• Simon Kessler,
• Peter S. Solomon,
• Andrew M. Piggott and
• Yit-Heng Chooi

Beilstein J. Org. Chem. 2019, 15, 2020–2028, doi:10.3762/bjoc.15.198

• biosynthetic gene cluster (tpc) for terpestacin (12) has been recently identified from Bipolaris maydis [36]. A didomain sesterterpene synthase (tpcA) with a terpene cyclase domain and polyprenyltransferase domain was demonstrated to be responsible for the production of the sesterterpene backbone of 12. A

• (tpcB and tpcC) encoded in the tpc cluster as COCSADRAFT_342924 (92% identity) and COCSADRAFT_146541 (98% identity), respectively, while the tpcD homolog in B. sorokiniana corresponded to COCSADRAFT_94398 (91% identity). This suggests that the homologous gene cluster in B. sorokiniana is likely

Genomics-inspired discovery of massiliachelin, an agrochelin epimer from Massilia sp. NR 4-1

• Jan Diettrich,
• Hirokazu Kage and
• Markus Nett

Beilstein J. Org. Chem. 2019, 15, 1298–1303, doi:10.3762/bjoc.15.128

• , unveiled the genetic basis of its biosynthesis. Results and Discussion The micacocidin-type BGC from Massilia sp. NR 4-1 and its enzymatic assembly line are depicted in Figure 1A and 1B. The gene cluster covers 34.7 kbp of contiguous DNA and includes ten genes (RS02190-RS02235), of which seven have

• cluster from Massilia sp. NR 4-1 (top) and of the mic gene cluster from R. solanacearum GMI1000 (bottom). The open reading frames are color-coded according to their predicted function. B) Domain architecture of the massiliachelin (top) and the micacocidin (bottom) assembly lines. Domain notation: FAAL

• array detector. In total, 12.0 mg of 1 were isolated. Massiliachelin (1) pale yellow solid; UV (MeOH) λmax (log ε): 356 (3.06), 280 (4.18), 228 (4.64) nm; 1H and 13C NMR, Table 1; HRESIMS m/z: [M + H]+, calcd for C23H35N2O4S2, 467.2033; found, 467.2033. A) Organization of the micacocidin-type gene

New terpenoids from the fermentation broth of the edible mushroom Cyclocybe aegerita

• Frank Surup,
• Florian Hennicke,
• Nadine Sella,
• Maria Stroot,
• Steffen Bernecker,
• Sebastian Pfütze,
• Marc Stadler and
• Martin Rühl

Beilstein J. Org. Chem. 2019, 15, 1000–1007, doi:10.3762/bjoc.15.98

• clusters. Keywords: bioinformatics; gene cluster analysis; natural products; secondary metabolites; structure elucidation; terpenes; Introduction The basidiomycete Agrocybe aegerita (synonym: A. cylindracea) was traditionally accommodated in the genus Agrocybe (family Bolbitiaceae) until a recent

• of C. aegerita [16], two putative sesquiterpene synthase gene clusters have been identified on the basis of the published Δ6-protoilludene gene cluster of Omphalotus olearius [17]. The protein sequences of the genes clustering adjacent to the putative sesquiterpene synthase genes going by the gene

Synthesis and SAR of the antistaphylococcal natural product nematophin from Xenorhabdus nematophila

• Frank Wesche,
• Hélène Adihou,
• Thomas A. Wichelhaus and
• Helge B. Bode

Beilstein J. Org. Chem. 2019, 15, 535–541, doi:10.3762/bjoc.15.47

• -phenylethylamine derivative 2 with an α-keto amide moiety, which could be identified upon heterologous expression of the appropriate gene cluster in E. coli [15]. Moreover, elongated nematophin derivatives, namely nevaltophins from Xenorhabdus PB62.4, were described incorporating an additional valine. As 1 and

Chemical structure of cichorinotoxin, a cyclic lipodepsipeptide that is produced by Pseudomonas cichorii and causes varnish spots on lettuce

• Hidekazu Komatsu,
• Takashi Shirakawa,
• Takeo Uchiyama and
• Tsutomu Hoshino

Beilstein J. Org. Chem. 2019, 15, 299–309, doi:10.3762/bjoc.15.27

• gene cluster. Differences in the 13C signal intensities were a little in the feeding experiments using L- or D-[1-13C]-Ala (see Figure S20D and S20E, Supporting Information File 1). These results indicated that an epimerase is involved in the biosynthetic gene cluster of this strain. Thus, we failed to

• assign the D or L configurations for all the amino acids by the feeding experiments. However, we succeeded in proposing the complete stereochemistry of the molecule by careful analysis of the biosynthetic gene cluster (nonribosomal peptide synthetases, NRPS). These results will be reported in due course

The enzymes of microbial nicotine metabolism

• Paul F. Fitzpatrick

Beilstein J. Org. Chem. 2018, 14, 2295–2307, doi:10.3762/bjoc.14.204

• in P. putida S16 was originally identified as a 6-hydroxy-3-succinoylpyridine hydroxylase catalyzing the formation of 2,5-dihydroxypyridine from 6-hydroxy-3-succinoylpyridine based on the location of the gene in a gene cluster that conferred on E. coli the ability to degrade nicotine to 2,5

• enzyme has been isolated from Pseudomonas sp. ZZ-5 [60]. The subsequent steps in metabolism of 2,5-dihydropyridine by P. putida S16 were identified when the gene cluster nic2 that contained hspb was sequenced, with the demonstration that incorporation of nic2 into E. coli allowed cells to convert 6

• -formylmaleamate, the same reaction as is catalyzed by the dioxygenase Hpo from P. putida S16. In Sphingomonas melonis TY, the genes for the metabolism of nicotine are found in the ndp gene cluster [65]. The mRNA levels for ndpA-H all increase 10 to 100-fold upon growth in the presence of nicotine. Sequence

Lanyamycin, a macrolide antibiotic from Sorangium cellulosum, strain Soce 481 (Myxobacteria)

• Lucky S. Mulwa,
• Rolf Jansen,
• Dimas F. Praditya,
• Kathrin I. Mohr,
• Patrick W. Okanya,
• Joachim Wink,
• Eike Steinmann and
• Marc Stadler

Beilstein J. Org. Chem. 2018, 14, 1554–1562, doi:10.3762/bjoc.14.132

• on its biosynthesis and comparison of the homology of the respective gene clusters appear interesting in order to address the hypothesis that a horizontal gene transfer of the biosynthesis gene cluster between an actinobacterium and a myxobacterium may have occurred. Experimental General experimental

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

• only, instead of a mixture of desulfoclethramycin and clethramycin. The mediomycin gene cluster does not encode an amidinohydrolase, but when three candidate amidinohydrolase genes from elsewhere in the S. mediocidicus genome were individually expressed in Escherichia coli and assayed, only one of them

• (medi4948), located 670 kbp away from the mediomycin gene cluster on the chromosome, catalysed the removal of the amidino group from desulfoclethramycin. Subsequent cloning of medi4948 into DSM4137 caused mediomycins A and B to accumulate at the expense of clethramycin and desulfoclethramycin, respectively

• antibiotics primycin and desertomycin [10] but not in the reported cluster for mediomycin in S. blastmyceticus [8], so the enzyme hypothesised to be responsible for this step in mediomycin biosynthesis has not been identified until now. We present here the characterisation of the med biosynthetic gene cluster

Biosynthetic origin of butyrolactol A, an antifungal polyketide produced by a marine-derived Streptomyces

• Enjuro Harunari,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2017, 13, 441–450, doi:10.3762/bjoc.13.47

• -labeling result, this labeling pattern suggested that the carbons from C-1 to C-8 are derived from hydroxymalonyl-ACP. This conclusion is supported by the sequencing analysis of the gene cluster for butyrolactol biosynthesis (Figure 5, Table 2). Four genes coding homologues of enzymes involved in

• conclusion is consistent with our previous bioinformatic prediction that suggested the presence of genes necessary for the supply of hydroxymalonyl-ACP adjacent to the PKS gene cluster of the butyrolactol biosynthesis. The results obtained in this study provide useful information for further biosynthetic

• -butyl group. Actinomycete metabolites possessing a contiguous 1,2-diol system. Feeding experiments of 13C-labeled precursors into 1 detected by 2D-INADEQUATE NMR experiments. (a) [1,2-13C2]acetate; (b) [U-13C6]glucose. Organization of the biosynthesis gene cluster for 1. Blue, transcriptional regulator

Solid-phase enrichment and analysis of electrophilic natural products

• Frank Wesche,
• Yue He and
• Helge B. Bode

Beilstein J. Org. Chem. 2017, 13, 405–409, doi:10.3762/bjoc.13.43

• been detected from infected insects [25], low-salt growth media [24] or by heterologous expression of the respective gene cluster in E. coli [26]. Their identification in this study was confirmed with pure glidobactin A (4) showing the same azide reactivity and retention time compared to 4 from the

Posttranslational isoprenylation of tryptophan in bacteria

• Masahiro Okada,
• Tomotoshi Sugita and
• Ikuro Abe

Beilstein J. Org. Chem. 2017, 13, 338–346, doi:10.3762/bjoc.13.37

• of the natural competence of B. subtilis revealed that the comQXPA gene cluster was responsible for B. subtilis to induce the genetic competence involved in the secretion of the ComX pheromone (Figure 4A) [13][21][25]. ComQ, the first protein encoded in the cluster, functions as an

• scaffold as that of the ComX pheromones, but with the opposite stereochemistry [54]. The KgpA to G gene cluster was identified as encoding the kawaguchipeptins synthase in M. aeruginosa NIES-88 [55]. KgpF is a member of the ABBA prenyltransferase family, which shares a common structural motif known as the

A non-canonical peptide synthetase adenylates 3-methyl-2-oxovaleric acid for auriculamide biosynthesis

• Daniel Braga,
• Dirk Hoffmeister and
• Markus Nett

Beilstein J. Org. Chem. 2016, 12, 2766–2770, doi:10.3762/bjoc.12.274

• ]. Retrobiosynthetic analysis allowed the identification of a 14,130 bp-gene cluster, now referred to as aul-cluster (Figure 2), which putatively encodes two NRPSs (AulA and AulB) and one PKS (AulC) possessing domains that collectively allow and plausibly explains the assembly of 1. A gene for a type-II thioesterase

• analogues as potential new drug candidates. Herpetosiphon natural products auriculamide (1) and siphonazole (2). Organisation of the aul biosynthetic gene cluster. Circles illustrate the domain architecture of the NRPSs and the PKS present therein. Domains are abbreviated as A, adenylation; ACP, acyl

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

• (marginolactones) azalomycin and kanchanamycin, isolated respectively from Streptomyces malaysiensis DSM4137 and Streptomyces olivaceus Tü4018, the first extension module catalyses both the first and second cycles of polyketide chain extension. To confirm the integrity of the azl gene cluster, it was cloned intact

• gene cluster for biosynthesis of the polyketide β-lactone ebelactone in Streptomyces aburaviensis has shown that, contrary to a recently-published proposal, the ebelactone polyketide synthase faithfully follows the colinear modular paradigm. Keywords: colinearity; ebelactone; enzyme catalysis

• which it influences the structures of complex polyketides. We aimed to characterise three recently uncovered candidates for iterative operation within a modular PKS, based on sequencing of the structural genes showing fewer modules present in the gene cluster than required to furnish the observed

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

• formation of up to two new stereocentres. Its appearance in several polyketide biosynthetic pathways was proposed for a decade based on gene cluster analysis. An in vitro characterisation of responsible catalytic units has however only recently been achieved. Two pyran-forming cyclase domains were

• ]. The actinorhodin (34) PKS is probably the best studied type II PKS and has been used as a model system for understanding basic features of such iterative bacterial systems. The respective biosynthetic gene cluster had already been cloned in 1984 and the genes were sequenced in 1992 (Scheme 6) [23][24

• ) AlnT and the flavin reductase AlnH [33]. No 3HAD homolog is present in the gene cluster that could catalyse a similar reaction as in the above mentioned examples. Instead, the oxidoreductase AlnO was proposed to catalyse the stereoselective reduction of the ketone at C15 in 49. The pyran 51 would then

The EIMS fragmentation mechanisms of the sesquiterpenes corvol ethers A and B, epi-cubebol and isodauc-8-en-11-ol

• Patrick Rabe and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2016, 12, 1380–1394, doi:10.3762/bjoc.12.132

• the actinobacterium Micromonospora aurantiaca [9] and more than 30 blastmycinones, a class of γ-lactones that depend on the antimycin biosynthetic gene cluster in several streptomycetes [10]. We have also recently developed structural proposals for a series of methylated monoterpenes from the 2

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

• for a number of characterised secondary metabolite pathways. For example, the bottromycin gene cluster encodes two stand-alone YcaO domain proteins that have been postulated to participate in heterocyclisation reactions [10][11][12][13]. Lanthionine bond formation in lanthipeptides Lanthipeptides

• inform the characterisation of primary metabolism. Surprisingly, the gene cluster for the AviCys-containing RiPP cypemycin indicates that this pathway features an alternative way to produce dehydrated amino acids [65]. Firstly, the cluster does not encode any Lan-like dehydratases, and secondly, the Dha

• piperidine ring [69] (Figure 6A). Micrococcin was the first member to be identified [70], while the most well-studied member of the class is thiostrepton [71], whose gene cluster was the first of this class to be reported [72][73], along with the thiocillin and siomycin A gene clusters [73][74]. Thiopeptides

Marine-derived myxobacteria of the suborder Nannocystineae: An underexplored source of structurally intriguing and biologically active metabolites

• Antonio Dávila-Céspedes,
• Peter Hufendiek,
• Max Crüsemann,
• Till F. Schäberle and
• Gabriele M. König

Beilstein J. Org. Chem. 2016, 12, 969–984, doi:10.3762/bjoc.12.96

• gene clusters, among them three NRPS, two PKS, three NRPS/PKS and four ribosomal peptides (see Table 1). Apart from homologies to geosmin (100%), aurafuron (71%) and paneibactin (50%) biosynthetic genes, the gene clusters display a large degree of novelty. Recently, the biosynthetic gene cluster of

• the producing strain SWB007. The results revealed a PKS III gene cluster adjacent to a halogenase sequence (unpublished data). Upon sequencing, primers for these genes were designed. Given the genetic proximity among the E. salina isolates, strains SWB004, SWB005 and SWB006 were screened with the PKS

• synthesis of NRPS, PKS and hybrid NRPS-PKS products (see Table 1). Apart from the geosmin biosynthesis genes, no gene cluster or fragment thereof shares an identity higher than 33% to any known gene cluster in the MiBIG database [64]. It should be noted that since this is a draft genome sequence, the actual

Muraymycin nucleoside-peptide antibiotics: uridine-derived natural products as lead structures for the development of novel antibacterial agents

• Daniel Wiegmann,
• Stefan Koppermann,
• Marius Wirth,
• Giuliana Niro,
• Kristin Leyerer and
• Christian Ducho

Beilstein J. Org. Chem. 2016, 12, 769–795, doi:10.3762/bjoc.12.77

• ]. Biosynthesis So far, there are only limited insights into muraymycin biosynthesis. The biosynthetic gene cluster for the formation of muraymycins in Streptomyces sp. NRRL 30471 has been identified by Chen, Deng et al. in 2011 [118]. The sequence analysis revealed the cluster to contain 33 open reading frames

• (ORFs) with 26 of them being involved in muraymycin formation. Based on their elucidation of the gene cluster and sequence homologies, Chen, Deng et al. proposed an outline pathway for muraymycin biosynthesis (Scheme 10). According to this biosynthetic proposal, uridine (1) is enzymatically oxidised to

• dioxygenase Mur16 to catalyse β-hydroxylations of two structurally distinct amino acid substrates, i.e., L-arginine (106) and thioester-activated L-leucine 112. As pointed out, there is a lack of experimental insights into muraymycin biosynthesis beyond the elucidation of its gene cluster. However, Van Lanen

Antibiotics from predatory bacteria

• Juliane Korp,
• María S. Vela Gurovic and
• Markus Nett

Beilstein J. Org. Chem. 2016, 12, 594–607, doi:10.3762/bjoc.12.58

• reaction [109][110]. The althiomycin biosynthetic gene cluster was recently identified in M. xanthus DK897 by a combination of retrobiosynthetic analysis and gene inactivation [111]. Two open reading frames (ORFs) encoding for a nonribosomal peptide synthetase (NRPS) and a NRPS/polyketide synthase (PKS

• cystobactamid biosynthesis gene cluster led to the identification of a gene encoding a putative resistance factor. This discovery was the starting point for resolving the molecular target of these antibiotics. Subsequent assays confirmed that the cystobactamids act as bacterial DNA gyrase inhibitors [113

• metabolites from the H. aurantiacus type strain 114-95T led to the discovery of auriculamide (22) [127]. This natural product is composed of a 2-hydroxy-3-methylvalerate and a 2-amino-1-(3-chloro-4-hydroxyphenyl)pentan-3-one residue. A retrobiosynthetic analysis allowed the assignment of the gene cluster

Biosynthesis of α-pyrones

• Till F. Schäberle

Beilstein J. Org. Chem. 2016, 12, 571–588, doi:10.3762/bjoc.12.56

• lactonization at the ACP-bound terminus yields the pyrone ring. As an example the enterocin (76, Figure 19) biosynthesis will be regarded (Figure 20). In the marine bacterium Streptomyces maritimus a gene cluster corresponding to enterocin (enc) biosynthesis was identified [81]. The minimal enc PKS, EncABC, is

Natural products from microbes associated with insects

• Christine Beemelmanns,
• Huijuan Guo,
• Maja Rischer and
• Michael Poulsen

Beilstein J. Org. Chem. 2016, 12, 314–327, doi:10.3762/bjoc.12.34

• molecular analysis of the biosynthetic gene cluster of pederin (3) [49][50][51][52]. Beetle larvae hatching from pederin-containing eggs were less prone to predation by wolf spiders than pederin-free larvae, indicating the ecological significance of this secondary metabolite [53]. The biosynthetic gene

• displayed negative effects on the growth of the antagonistic fungus O. minus. By genetic analysis and manipulation of the producing Streptomyces strain the respective biosynthetic gene cluster could be identified. It encodes a hybrid polyketide synthase–non-ribosomal peptide synthase (PKS–NRPS), and

• cluster analysis also revealed that pederin is formed by an enzyme belonging to a functionally and evolutionarily novel group termed trans-acyltransferase PKSs (trans-AT PKSs) [24][52]. The structurally related compound diaphorin (4) was later found in a study of the defensive symbiosis between the Asian

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

• the product of a polyketide biosynthetic gene cluster [24]. To test whether N-acetylcysteine could be a biosynthetic precursor of the unusual 1,5-oxathiocane structure, feeding experiments using both (2S)- and (2R)-N-((2H3)acetyl)cysteine were performed. The deuterium atoms of both precursors were

• , the first structurally characterized bacterial diterpene cyclase [66]. After identification of the biosynthetic gene cluster, a mechanism involving a deprotonation–reprotonation sequence and two 1,2-hydride shifts was proposed [67]. However, a simple feeding experiment performed with a S. albus