Discovery and biosynthesis of bacterial drimane-type sesquiterpenoids from Streptomyces clavuligerus

• Dongxu Zhang,
• Wenyu Du,
• Xingming Pan,
• Xiaoxu Lin,
• Fang-Ru Li,
• Qingling Wang,
• Qian Yang,
• Hui-Min Xu and
• Liao-Bin Dong

Beilstein J. Org. Chem. 2024, 20, 815–822, doi:10.3762/bjoc.20.73

• significant in industrial applications, renowned for its production of diverse natural products with chemical structures and bioactivities, such as cephamycin C, clavulanic acid, and isopenicillin N [22][23][24]. Genomic sequencing of S. clavuligerus has revealed 48 potential secondary metabolite BGCs, and

Methodology for awakening the potential secondary metabolic capacity in actinomycetes

• Shun Saito and
• Midori A. Arai

Beilstein J. Org. Chem. 2024, 20, 753–766, doi:10.3762/bjoc.20.69

• , and the associated undiscovered secondary metabolite biosynthesis genes are called “silent” genes. This review outlines several approaches to further activate the metabolic potential of actinomycetes. Keywords: actinomycete; co-culture; heat shock metabolites (HSMs); secondary metabolites; silent

• considered to have been completely characterized. This may be because the number of discovered compounds is small compared to the number of secondary metabolite biosynthesis genes harbored by actinomycetes [26][27][28]. For example, in Streptomyces avermitilis, 38 secondary metabolite biosynthetic gene

• identified. These as yet undiscovered secondary metabolite biosynthesis genes are called “silent genes”, because they are either not expressed or their expression levels are low under normal culture conditions. A number of studies have reported methods to activate these genes, and many new compounds have

New variochelins from soil-isolated Variovorax sp. H002

• Jabal Rahmat Haedar,
• Aya Yoshimura and
• Toshiyuki Wakimoto

Beilstein J. Org. Chem. 2024, 20, 692–700, doi:10.3762/bjoc.20.63

• , including soil-isolated plant pathogens. Results and Discussion Isolation and structure elucidation In this study, we explored the secondary metabolite potential of the soil-isolated Variovorax sp. H002, domesticated from the Medicinal Plant Garden of the Faculty of Pharmaceutical Sciences, Hokkaido

Discovery of unguisin J, a new cyclic peptide from Aspergillus heteromorphus CBS 117.55, and phylogeny-based bioinformatic analysis of UngA NRPS domains

• Sharmila Neupane,
• Marcelo Rodrigues de Amorim and
• Elizabeth Skellam

Beilstein J. Org. Chem. 2024, 20, 321–330, doi:10.3762/bjoc.20.32

• those from UngA’ regardless of which two amino acids were condensed. Conclusion In this study unguisins B and J were isolated from A. heteromorphus CBS 117.55 which has not been extensively investigated for secondary metabolite production. A BGC encoding the unguisins was identified by genome mining

Identification of the p-coumaric acid biosynthetic gene cluster in Kutzneria albida: insights into the diazotization-dependent deamination pathway

• Seiji Kawai,
• Akito Yamada,
• Yohei Katsuyama and
• Yasuo Ohnishi

Beilstein J. Org. Chem. 2024, 20, 1–11, doi:10.3762/bjoc.20.1

• vigorously used to search for novel compounds in recent years due to the rapid improvement of DNA sequence technologies and computational approaches to analyze BGCs [1][3]. Our research group previously identified the secondary metabolite-specific nitrous acid biosynthetic pathway, named ANS (aspartate

Combining the best of both worlds: radical-based divergent total synthesis

• Kyriaki Gennaiou,
• Antonios Kelesidis,
• Maria Kourgiantaki and
• Alexandros L. Zografos

Beilstein J. Org. Chem. 2023, 19, 1–26, doi:10.3762/bjoc.19.1

• meroterpenoids. This class of compounds possesses versatile bioactivities, ranging from anticancer and anti-HIV to antifungal properties, with minor modifications on the decoration of either the hydroquinone or the terpene part of the secondary metabolite [34]. The group applied a semisynthetic plan starting

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

• ). Moreover, since these assembly line-like pathways follow the same biosynthetic principle, they often form hybrids with other biosynthetic assembly line-like pathways [21]. Prominent examples of the usage of pHMMs are the original algorithm of the antibiotics & Secondary Metabolite Analysis Shell (antiSMASH

• secondary metabolite biosynthetic enzymes are distant paralogs of enzymes involved in primary metabolism [63][71]. These NP biosynthetic enzymes are hypothesized to have undergone significant sequence and selectivity changes while still operating based on the same reaction mechanism (e.g., fatty acid

• genome-wide characterization of all clustered genes (gcBGC). In comparison to state-of-the-art genome mining tools, gcBGC inverts the current BGC identification process. Instead of identifying NP BGCs, all clustered genes involved in primary and secondary metabolite biosynthesis are identified. To

Unsaturated fatty acids and a prenylated tryptophan derivative from a rare actinomycete of the genus Couchioplanes

• Shun Saito,
• Kanji Indo,
• Naoya Oku,
• Hisayuki Komaki,
• Masashi Kawasaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2021, 17, 2939–2949, doi:10.3762/bjoc.17.203

• underexplored. However, in silico genome mining identified multiple secondary metabolite biosynthetic gene clusters in selected strains from minor actinomycetes genera, implying their comparable biosynthetic capacities to those of the already proven genera [19]. Encouraged by these reports, we examined the

• Micromonosporaceae first isolated in 1994 from a sandy soil in Japan [23], was set to be the next target. While the anti-SMASH-assisted genome mining [24] in C. caeruleus DSM 43634 revealed approximately 20 secondary metabolite biosynthetic gene clusters, only one compound, heptaene macrolide 67-121C, is known to

α-Ketol and α-iminol rearrangements in synthetic organic and biosynthetic reactions

• Scott Benz and
• Andrew S. Murkin

Beilstein J. Org. Chem. 2021, 17, 2570–2584, doi:10.3762/bjoc.17.172

• similarity in reaction, 1-deoxy-ᴅ-xylulose-5-phosphate reductoisomerase (DXR) instead uses a retro-aldol/aldol sequence to accomplish its rearrangement of 68 to 69. c) The secondary metabolite aurachin C (71) is oxidized by the FAD-dependent monooxygenase AuaG to epoxide 72, which upon deprotonation by an

Catalyzed and uncatalyzed procedures for the syntheses of isomeric covalent multi-indolyl hetero non-metallides: an account

• Ranadeep Talukdar

Beilstein J. Org. Chem. 2021, 17, 2102–2122, doi:10.3762/bjoc.17.137

• the indoles are less studied compared to the same through their pyrrole counterpart. The corresponding compounds are investigated for boron, nitrogen, oxygen, sulfur, and selenium as the central connecting atom. Boranes The indole alkaloid dragmacidin D is a marine secondary metabolite which was

Natural products in the predatory defence of the filamentous fungal pathogen Aspergillus fumigatus

• Jana M. Boysen,
• Nauman Saeed and
• Falk Hillmann

Beilstein J. Org. Chem. 2021, 17, 1814–1827, doi:10.3762/bjoc.17.124

• metabolites. The genetic potential for the production of secondary metabolites in fungi is high and numerous potential secondary metabolite gene clusters have been identified in sequenced fungal genomes. Their production may well be regulated by specific ecological conditions, such as the presence of

• human pathogenic fungi like A. fumigatus, one of the most common airborne fungal pathogens, might lead to new insight in virulence mechanisms and the role of SMs therein [32]. The aim of this review is to depict the fungal secondary metabolite potential and its role in an ecological context using A

• mycotoxins (A. flavus) or can cause severe infections (A. fumigatus, A. terreus). Despite their different role for humans, they commonly share a high potential for the production of secondary metabolites, measured by the predicted number of secondary metabolite gene clusters identified by numerous genome

Analogs of the carotane antibiotic fulvoferruginin from submerged cultures of a Thai Marasmius sp.

• Birthe Sandargo,
• Leon Kaysan,
• Rémy B. Teponno,
• Christian Richter,
• Benjarong Thongbai,
• Frank Surup and
• Marc Stadler

Beilstein J. Org. Chem. 2021, 17, 1385–1391, doi:10.3762/bjoc.17.97

• Marasmius spp. include the cryptoporic acids [4], marasmals, marasmones, and oreadones [5][6], the caryophyllane hebelophyllene C [7], and the carotane fulvoferruginin (1) [8] (Figure 1). The latter is the only known secondary metabolite from M. fulvoferrugineus Gilliam and displays a modest antibiotic and

Nocarimidazoles C and D, antimicrobial alkanoylimidazoles from a coral-derived actinomycete Kocuria sp.: application of ¹J_C,H coupling constants for the unequivocal determination of substituted imidazoles and stereochemical diversity of anteisoalkyl chains in microbial metabolites

• Md. Rokon Ul Karim,
• Enjuro Harunari,
• Amit Raj Sharma,
• Naoya Oku,
• Kazuaki Akasaka,
• Daisuke Urabe,
• Mada Triandala Sibero and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 2719–2727, doi:10.3762/bjoc.16.222

• habitat [6][7]. Their secondary metabolite machinery is activated in the sea, as indicated by the isolation of enediyne antitumor antibiotics from marine invertebrates. Namenamicin [8] and the shishijimicins [9], the chalicheamicin-type enediyne polyketides, were isolated from a colonial tunicate. These

A cyclopeptide and three oligomycin-class polyketides produced by an underexplored actinomycete of the genus Pseudosporangium

• Shun Saito,
• Kota Atsumi,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Naoya Oku,
• Md. Rokon Ul Karim,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1100–1110, doi:10.3762/bjoc.16.97

• widely used as an indicator of the taxonomic position of prokaryotes. It was believed that a high similarity of the 16S rRNA gene sequence implied the closeness or even the identity in other sets of genes including secondary metabolite biosynthetic genes. However, our recent analysis of Streptomyces

• species demonstrated that the distribution of secondary metabolite biosynthetic genes was not the same even in phylogenetically close species [11]. This finding became our starting point to explore the secondary metabolism in actinomycete genera from which no secondary metabolites were described. “Rare

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

• of fabclavines as major antibiotics in several entomopathogenic strains, our work lays the foundation for the rapid fabclavine identification and dereplication as the basis for future work of this widespread and bioactive SM class. Keywords: antibiotic; fabclavine; NRPS-PKS hybrid; secondary

• metabolite; Xenorhabdus; Introduction The constantly increasing threat of multiresistant pathogens requires the development of new antibiotics, as they are indispensable to maintain the state of health of our society [1]. Bacterial natural products, also called secondary or specialized metabolites (SM

Pigmentosins from Gibellula sp. as antibiofilm agents and a new glycosylated asperfuran from Cordyceps javanica

• Soleiman E. Helaly,
• Wilawan Kuephadungphan,
• Patima Phainuphong,
• Mahmoud A. A. Ibrahim,
• Kanoksri Tasanathai,
• Suchada Mongkolsamrit,
• Janet Jennifer Luangsa-ard,
• Souwalak Phongpaichit,
• Vatcharin Rukachaisirikul and
• Marc Stadler

Beilstein J. Org. Chem. 2019, 15, 2968–2981, doi:10.3762/bjoc.15.293

• bioactive secondary metabolites. Herein, we report on the isolation, structure elucidation, and biological activities of six compounds from Gibellula sp. and Cordyceps javanica. Furthermore, the species-specific patterns of secondary metabolite production were studied. Results and Discussion Structure

• the secondary metabolite production among species of Cordycipitaceae, HPLC–UV–vis profiles of all fungal isolates were generated and compared to each other. This revealed that the individual species possessed unique secondary metabolite profiles. Pigmentosins A (1) and B (2) were detected in all

• important role of chemotaxonomy in the modern taxonomy of fungi: 1) secondary metabolite profiles as high-informative data to support morphological and phylogenetic studies, 2) the success of using the polyphasic approach in species delimitation, and 3) the potency of chemotaxonomy in the discovery of

Two new aromatic polyketides from a sponge-derived Fusarium

• Mada Triandala Sibero,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Ocky K. Karna Radjasa,
• Agus Sabdono,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2019, 15, 2941–2947, doi:10.3762/bjoc.15.289

• polyketide; Fusarium; marine fungus; secondary metabolite; sponge; Introduction Marine organisms have been known as a potential source of prospective bioactive compounds, and sponges are particularly emphasized as the most promising source among all marine invertebrates [1][2]. However, the collection of

• metabolite of the fungus Geosmithia [24]. Plant metabolites, feralolide and its glycoside, possessing the same skeleton as 2 were reported from the medicinal herb Aloe vera [29], but this carbon skeleton is novel as a fungal secondary metabolite. Experimental General experimental procedures NMR spectra were

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

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

• synthetic biology to engineer pathways that will expand molecular diversity, especially around scaffolds associated with high-value compounds. The biosynthetic logic of terpene formation differs significantly from the logic employed by other classes of secondary metabolite biosynthetic pathways. Bacterial

• lividans, under the control of exogenous promoters [92][93][94]. To minimize the cellular resource competition and facilitate cleaner analysis, many of these hosts have been engineered to remove native secondary-metabolite BGCs and for optimized terpene precursor supply [1][95][96][97]. Like Streptomyces

Skeletocutins M–Q: biologically active compounds from the fruiting bodies of the basidiomycete Skeletocutis sp. collected in Africa

• Tian Cheng,
• Clara Chepkirui,
• Cony Decock,
• Josphat C. Matasyoh and
• Marc Stadler

Beilstein J. Org. Chem. 2019, 15, 2782–2789, doi:10.3762/bjoc.15.270

• , there are only few examples where the same compounds were predominant in both. For instance, in most species hitherto studied of the ascomycete order Xylariales, the fruiting bodies and cultures mostly showed a complementary secondary metabolite production [7]. In the current case, it appears that the

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

• library (>7,100 standards) also failed to provide a single known secondary metabolite, further suggesting the strain was a hitherto unaccounted species of Aspergillus. A. nanangensis was cultivated separately on jasmine rice and pearl barley for 21 days, which resulted in confluent and thick mycelial

• section Usti [17]. Here, we showed for the first time that an Aspergillus species from the section Jani produces such drimane sesquiterpenoids and has a secondary metabolite repertoire that is distinct from close members in the section Jani. Comparative analysis identified a group of putative homologous

• liquid media flasks on a shaker pad rotating at 90 rpm. The grains and agar cultivars were sub-sampled on days 7, 14 and 21, while the liquids were sub-sampled on day 7. The sub-samples were extracted in MeOH for 2 h prior to being analysed by analytical HPLC (C18) to determine the secondary metabolite

Isolation of fungi using the diffusion chamber device FIND technology

• Benjamin Libor,
• Henrik Harms,
• Stefan Kehraus,
• Ekaterina Egereva,
• Max Crüsemann and
• Gabriele M. König

Beilstein J. Org. Chem. 2019, 15, 2191–2203, doi:10.3762/bjoc.15.216

• environment. Halotolerance was to date exclusively reported for members of the Cladosporium sphaerospermum complex [28]. Analysis of genes involved in secondary metabolite production suggested Cadophora malorum as a producer of bioactive compounds [29], as later confirmed by the results of Almeida et al. [30

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

• domain organization of the two corresponding biosynthetic assembly lines further indicated that Massilia sp. NR 4-1 does not produce micacocidin, but a derivative of this secondary metabolite. The isolation of siderophores from microorganisms is usually straightforward due to their iron-dependent

Phylogenomic analyses and distribution of terpene synthases among Streptomyces

• Lara Martín-Sánchez,
• Kumar Saurabh Singh,
• Mariana Avalos,
• Gilles P. van Wezel,
• Jeroen S. Dickschat and
• Paolina Garbeva

Beilstein J. Org. Chem. 2019, 15, 1181–1193, doi:10.3762/bjoc.15.115

• [33]. Therefore, these results could also be interpreted as evidence for a rapid evolution of secondary metabolite genes to create new natural products with beneficial ecological functions for the producing organism. While many streptomycetes produce geosmin as a major metabolite of their bouquets of

• transfers of terpene synthase genes in Streptomyces, but could also point to secondary metabolite genes as being less conserved than housekeeping (primary metabolism) genes. Rapid evolution of secondary metabolism can lead to new natural products with advanced ecological functions in specific ecological

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

• secondary metabolite profiles of C. aegerita, we found several terpenoids in submerged cultures. Aside from the main metabolite, bovistol (1), two new bovistol derivatives B and C (2, 3) and pasteurestin C as a new protoilludane (4) were isolated by preparative HPLC. Their structures were elucidated by mass