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

• genome mining and heterologous expression, we identified a cav biosynthetic gene cluster responsible for the biosynthesis of DMTs 2–4, along with a P450, CavA, responsible for introducing the C-2 and C-3 hydroxy groups. Furthermore, the substrate scope of CavA revealed its ability to hydroxylate drimenol

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

• , genome mining of the marine actinomycete Streptomyces seoulensis A01 enabled the identification of a giant type I polyketide synthase gene cluster (asm) [30]. Heterologous expression of the cryptic asm cluster using a bacterial artificial chromosome vector in a heterologous host led to the production of

Genome mining of labdane-related diterpenoids: Discovery of the two-enzyme pathway leading to (−)-sandaracopimaradiene in the fungus Arthrinium sacchari

• Fumito Sato,
• Terutaka Sonohara,
• Shunta Fujiki,
• Akihiro Sugawara,
• Yohei Morishita,
• Taro Ozaki and
• Teigo Asai

Beilstein J. Org. Chem. 2024, 20, 714–720, doi:10.3762/bjoc.20.65

• underexplored family of natural products. In the biosynthesis of fungal LRDs, bifunctional terpene cyclases (TCs) consisting of αβγ domains are generally used to synthesize the polycyclic skeletones of LRDs. Herein, we conducted genome mining of LRDs in our fungal genome database and identified a unique pair of

• of TCs in fungi. Keywords: diterpenoids; fungi; genome mining; labdane; terpene cyclase; Introduction Terpenoids are a structurally diverse family of natural products, including more than 80,000 compounds [1]. In the biosynthesis of terpenoids, terpene cyclases (TCs) add structural diversity and

• proposed to be derived from the early fusion of bacterial class I and II enzymes [3][15]. Fungal genomes contain a number of biosynthetic genes that are attractive targets for genome mining of novel natural products and biosynthetic enzymes [16][17][18]. In our research group, genome-guided exploration of

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

• aspartate residue as a query, Nett et al. performed genome mining of photoreactive siderophores and isolated two such siderophores, variochelins A and B, from the soil bacterium Variovorax boronicumulans [5]. The Variovorax spp. belonging to plant growth-promoting rhizobacteria (PGPR) enhance plant

A myo-inositol dehydrogenase involved in aminocyclitol biosynthesis of hygromycin A

• Michael O. Akintubosun and
• Melanie A. Higgins

Beilstein J. Org. Chem. 2024, 20, 589–596, doi:10.3762/bjoc.20.51

• family containing Hyg17 and discuss genome mining strategies that target this protein family to identify biosynthetic clusters for natural product discovery. Keywords: aminocyclitol; biosynthesis; hygromycin A; inositol dehydrogenase; myo-inositol; Introduction Hygromycin A is a natural product that

• Hyg17 sequences with other members of the oxidoreductase family and inositol dehydrogenases and discuss specialized genome mining approaches using these sequences to identify new natural product biosynthetic clusters. Results and Discussion Hyg17 enzyme activity We found that Hyg17 formed inclusion

• that contain these biosynthetic gene clusters could be producing a hygromycin A-like compound and further investigation is required. Genome mining for natural product biosynthetic clusters Since some enzymes from PF01408 are involved in natural product biosynthetic pathways, we wanted to see if

Recent developments in the engineered biosynthesis of fungal meroterpenoids

• Zhiyang Quan and
• Takayoshi Awakawa

Beilstein J. Org. Chem. 2024, 20, 578–588, doi:10.3762/bjoc.20.50

• they have similar substrate binding modes but different regional specificities. The rapid increase in genomic information has further expanded the number of available enzyme genes, thus increasing the potential for diversifying DMOA-derived meroterpenoid biosynthesis. Recently, a similar genome mining

• biosynthesis of bioactive compounds with still greater skeletal diversity. Conclusion In summary, many novel terpene cyclases and αKG-dependent dioxygenases were discovered by recent developments in genome mining approaches. Unique meroterpenoids have been generated by integrating these enzymes into

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

• 115571 which has relaxed substrate specificity in module 3. We performed genome mining of the publicly available A. heteromorphus CBS 117.55 (accession number MSFL00000000.1) [15] using fungiSMASH and identified a four gene BGC encoding a seven module NRPS, an alanine-racemase, a hydrolase, and a

• 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

• particular, actinomycetes, a major source of bioactive compounds, have numerous BGCs in their genomes, but the majority of them are thought to be silent under laboratory conditions [2]. Because these orphan BGCs are often related to the production of unknown natural products, genome mining has been

• [4]. To further understand the role of the ANS pathway in secondary metabolism, we recently identified the BGC for avenalumic acid (ava cluster, see the lower right corner of Figure 1B for its structure) by genome mining targeting the ANS pathway in Streptomyces sp. RI-77, and revealed its entire

• diazo group-containing compounds through directed evolution. Finally, this study is important because of the success of genome mining for BGCs in a rare actinomycete, K. albida. Although 47 BGCs were indicated in the K. albida genome by the antiSMASH analysis, only aculeximycin was reported as a natural

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

• sequencing technology has resulted in the introduction of an alternative approach towards novel natural product scaffolds: Genome mining. Genome mining is an in-silico natural product discovery strategy in which sequenced genomes are analyzed for the potential of the associated organism to produce natural

• developed for the biosynthetic rule-based identification of natural product gene clusters. Apart from these hard-coded algorithms, multiple tools that use machine learning-based approaches have been designed to complement the existing genome mining tool set and focus on natural product gene clusters that

• lack genes with conserved signature sequences. In this perspective, we take a closer look at state-of-the-art genome mining tools that are based on either hard-coded rules or machine learning algorithms, with an emphasis on the confidence of their predictions and potential to identify non-canonical

Characterization of a new fusicoccane-type diterpene synthase and an associated P450 enzyme

• Jia-Hua Huang,
• Jian-Ming Lv,
• Liang-Yan Xiao,
• Qian Xu,
• Fu-Long Lin,
• Gao-Qian Wang,
• Guo-Dong Chen,
• Sheng-Ying Qin,
• Dan Hu and
• Hao Gao

Beilstein J. Org. Chem. 2022, 18, 1396–1402, doi:10.3762/bjoc.18.144

• . Keywords: cytochrome P450 enzyme; diterpene synthase; gene cluster; genome mining; site-directed mutagenesis; Introduction Terpenoids are a large class of natural products that attract extensive attention, due to not only their potential applications in pharmaceuticals, agrochemicals, etc. but also due to

• , including traditional isolation from nature [5][6][7][8] and chemical synthesis [9], have been made to expand the structural diversity of FC-type diterpenoids for drug development. Along with the development of low-cost sequencing technologies and tractable heterologous expression systems, genome mining has

Cytochrome P450 monooxygenase-mediated tailoring of triterpenoids and steroids in plants

• Karan Malhotra and
• Jakob Franke

Beilstein J. Org. Chem. 2022, 18, 1289–1310, doi:10.3762/bjoc.18.135

• promiscuity which facilitates duplication events resulting in neofunctionalisation [15]. Ellarinacin (15) is a defence-related arborinane-type triterpenoid that was recently discovered in bread wheat (Triticum aestivum) by genome mining (Figure 6B) [26]. The ellarinacin gene cluster encodes the three CYP

• steroid metabolism, but also illustrate state-of-the-art approaches to discover and characterise new CYPs by genome mining, co-expression analyses, and efficient heterologous expression systems. Conclusion In this review, we provided a comprehensive overview over the phylogenetic distribution and diverse

New azodyrecins identified by a genome mining-directed reactivity-based screening

• Atina Rizkiya Choirunnisa,
• Kuga Arima,
• Yo Abe,
• Noritaka Kagaya,
• Kei Kudo,
• Hikaru Suenaga,
• Junko Hashimoto,
• Manabu Fujie,
• Noriyuki Satoh,
• Kazuo Shin-ya,
• Kenichi Matsuda and
• Toshiyuki Wakimoto

Beilstein J. Org. Chem. 2022, 18, 1017–1025, doi:10.3762/bjoc.18.102

• vitro assay elucidated the tailoring step of azodyrecin biosynthesis, which is mediated by the S-adenosylmethionine (SAM)-dependent methyltransferase Ady1. This study paves the way for the targeted isolation of aliphatic azoxy natural products through a genome-mining approach and further investigations

• the prediction of the producer of natural products with the functional groups of interest, leading to a higher rate of hits. We recently exploited genome mining targeting hydrazine synthetase and the generation of inorganic hydrazine N2H4 in acid hydrolysate as an indicator of N–N bond-containing

Structural basis for endoperoxide-forming oxygenases

• Takahiro Mori and
• Ikuro Abe

Beilstein J. Org. Chem. 2022, 18, 707–721, doi:10.3762/bjoc.18.71

• -based genome mining approach. While it is possible that many endoperoxide compounds are produced through non-enzymatic oxidation by ROS, future biosynthetic analyses of endoperoxide natural products will lead to the discovery of novel endoperoxide-forming pathways and generate more comprehensive

Tenacibactins K–M, cytotoxic siderophores from a coral-associated gliding bacterium of the genus Tenacibaculum

• Yasuhiro Igarashi,
• Yiwei Ge,
• Tao Zhou,
• Amit Raj Sharma,
• Enjuro Harunari,
• Naoya Oku and
• Agus Trianto

Beilstein J. Org. Chem. 2022, 18, 110–119, doi:10.3762/bjoc.18.12

• from 2.5 to 7.9 Mbp, biosynthetic gene clusters for siderophores, terpenes, and non-ribosomal peptides were identified by genome mining [39], suggesting a high capability of secondary metabolism in this genus. Further investigation is underway to disclose the actual diversity of metabolites from the

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

• .17.203 Abstract A genome mining survey combined with metabolome analysis of publicly available strains identified Couchioplanes sp. RD010705, a strain belonging to an underexplored genus of rare actinomycetes, as a producer of new metabolites. HPLC-DAD-guided fractionation of its fermentation extracts

• 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

On the mass spectrometric fragmentations of the bacterial sesterterpenes sestermobaraenes A–C

• Anwei Hou and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2020, 16, 2807–2819, doi:10.3762/bjoc.16.231

• bacterial sesterterpenes that were recently discovered by us from the actinomycete Streptomyces mobaraensis through a genome mining approach (Figure 1) [1]. All seven compounds are produced by a canonical terpene synthase, representing the first reported sesterterpene synthase of the classical type I from

• allows to identify interesting candidate genes coding for terpene synthases for further studies by genome mining. A major difficulty in the GC–MS-based identification of terpenes is associated with the high similarity of the mass spectra of structurally related terpenes. For this reason, the unambiguous

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

• Glomerella cingulata. All compounds showed moderate cytotoxicity against P388 murine leukemia cells with IC50 values in the micromolar to submicromolar ranges. These results exemplified the validity of phylogeny-focused strain selection combined with biosynthetic gene-directed genome mining for the efficient

• over 400 natural products [15], no secondary metabolites are reported from at least 24 genera. One such genus, Pseudosporangium, originally discovered from a sandy soil in Bangladesh in 2008 by Takahashi and co-workers [16], appeared promising, as genome mining in the draft sequence of P. ferrungineum

• , National Institute of Technology and Evaluation (NBRC), Kisarazu, Chiba 292-0818, Japan 10.3762/bjoc.16.97 Abstract Aside from the well-studied conventional actinomycetes such as Streptomyces, the less investigated genera of actinomycetes also represent a promising source of natural products. Genome

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

• (BGCs). While the antiSMASH database (online repository of BGCs predicted by the genome mining platform antiSMASH) lists more than 4,000 bacterial terpene BGCs [43], only 127 have been characterized and deposited in the MIBiG database (repository of characterized BGCs) to date (Figure 3) [44]. The

• comparatively small number of characterized bacterial terpenes can likely be attributed to three factors: 1) the early misconception that bacteria are not capable of producing complex terpenoids, 2) the lack of genome mining platforms for terpene biosynthetic gene clusters and the inability to perform rational

• NRPSs), bacterial TCs show only little overall sequence similarity [1]. The lack of conservation in primary sequence has slowed down our understanding of terpene cyclization and, as a result, hampered the development of efficient genome mining platforms for the detection of bacterial terpene BGCs

Genome mining in Trichoderma viride J1-030: discovery and identification of novel sesquiterpene synthase and its products

• Xiang Sun,
• You-Sheng Cai,
• Yujie Yuan,
• Guangkai Bian,
• Ziling Ye,
• Zixin Deng and
• Tiangang Liu

Beilstein J. Org. Chem. 2019, 15, 2052–2058, doi:10.3762/bjoc.15.202

• by genome mining and determined the structure of its corresponding products. One new 5/6 bicyclic sesquiterpene and its esterified derivative were characterised by GC–MS and 1D and 2D NMR spectroscopy. To the best of our knowledge, this is the first well-identified sesquiterpene synthase from T

• . viride to date. Keywords: genome mining; metabolic engineering; natural products; sesquiterpene synthase; terpenes; Trichoderma viride J1-030; Introduction Terpenoids represent the most diverse group of natural products, with a wide distribution in microorganisms, plants, insects and various marine

• . Four (10%) and eight (7%) membered ring structures (e.g. asteriscanolide) are seldom found [14]. With the lower costs of gene sequencing, recent developments in genome mining by sequencing and annotation have led to the discovery of a large number of functionally unknown terpene synthases [15][16][17

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

• product, which was named massiliachelin, corresponds to the assembly line encoded by the identified siderophore locus. Keywords: agrochelin; genome mining; Massilia; massiliachelin; siderophore; stereochemistry; Introduction In recent years, chemical investigations as well as genomics led to the

• production and complexing properties [15]. Therefore, we decided to initially focus our genome mining efforts on the micacocidin-type cluster in Massilia sp. NR 4-1. Here, we report the outcome of this study, which led to the identification of a previously unrecognized agrochelin epimer and, furthermore

Herpetopanone, a diterpene from Herpetosiphon aurantiacus discovered by isotope labeling

• Xinli Pan,
• Nicole Domin,
• Sebastian Schieferdecker,
• Hirokazu Kage,
• Martin Roth and
• Markus Nett

Beilstein J. Org. Chem. 2017, 13, 2458–2465, doi:10.3762/bjoc.13.242

• resemblance to cadinane-type sesquiterpenes from plants, but is structurally entirely unprecedented in bacteria. Based on its molecular architecture, a possible biosynthetic pathway is postulated. Keywords: genome mining; herpetopanone; Herpetosiphon; isotope labeling; terpene; Introduction Terpenoids

Opportunities and challenges for the sustainable production of structurally complex diterpenoids in recombinant microbial systems

• Katarina Kemper,
• Max Hirte,
• Markus Reinbold,
• Monika Fuchs and
• Thomas Brück

Beilstein J. Org. Chem. 2017, 13, 845–854, doi:10.3762/bjoc.13.85

• in diterpene biosynthetic routes entail time-consuming genome-mining and high-throughput screening technologies [64][65]. Additionally, the number of currently available, even partly annotated plant genomes and crystal structures of diterpene synthases is still limited. Yet, in order to establish

• diterpenes. Reprogramming the catalytic activities of (plant) diterpene synthases may also be an alternative to extensive genome-mining and screening strategies since this technique can potentially close or circumvent knowledge gaps in biosynthetic pathways to bioactive products which were previously

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

• studies and genome mining of structurally unique/novel secondary metabolites. Experimental General experimental procedures Sodium [1,2-13C2]acetate and L-valine-d8 were purchased from Cambridge Isotope Laboratories, Inc. [U-13C6]Glucose, sodium [1-13C]propionate, and L-[methyl-13C]methionine were

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

• chain, attached to the C3 of an oxidised isobenzofuran (Scheme 15). The respective biosynthetic cluster contains seven genes and has been identified by Wang and co-workers through a genome mining approach in Aspergillus nidulans [76]. Later on, the same group annotated a highly homologous gene cluster

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

• genome mining [155][156][157]. However, gene cluster identification does not provide detailed mechanistic information about post-translational modifications and there are numerous examples where key steps in pathways with sequenced gene clusters have not been characterised (see examples above). More

• ], although it is evident that many novel classes of RiPP await characterisation [7]. Despite the successes reported above, genome mining for novel RiPP clusters is hindered by a number of factors. Firstly, RiPP “gene clusters” can be as small as two genes: a precursor peptide and a tailoring protein