Chemical structure metagenomics of microbial natural products: surveying nonribosomal peptides and beyond

• Thomas Ma and
• John Chu

Beilstein J. Org. Chem. 2024, 20, 3050–3060, doi:10.3762/bjoc.20.253

• product to be amenable to the BGF workflow. Not only the microorganism of interest needs to be readily cultured, it must actively express its natural product biosynthetic gene cluster(s) (BGC) under laboratory culture conditions [18][19]. It turns out these pre-requisites are rarely met [16]. New

Chemo-enzymatic total synthesis: current approaches toward the integration of chemical and enzymatic transformations

• Ryo Tanifuji and
• Hiroki Oguri

Beilstein J. Org. Chem. 2024, 20, 1693–1712, doi:10.3762/bjoc.20.151

• 1970s, the biosynthetic pathway of 4 has been investigated through isotope labelling and analysis of metabolites from S. fradiae mutants [70][71][72][73]. Heterologous production of 4 was also achieved by expression of elucidated biosynthetic gene cluster from S. fradiae in Streptomyces venezuelae [74

• , they were faced with low expression levels of TylGV. To circumvent this problem, they employed the homologous enzymes JuvEIV and JuvEV from juvenimicin-producing Micromonospora chalcea subsp. izumensis [84][85]. The Juv gene cluster contained JuvEI–JuvEV with high homology to TylGI–TylGV, and P450

Methyltransferases from RiPP pathways: shaping the landscape of natural product chemistry

• Maria-Paula Schröder,
• Isabel P.-M. Pfeiffer and
• Silja Mordhorst

Beilstein J. Org. Chem. 2024, 20, 1652–1670, doi:10.3762/bjoc.20.147

• bioactivities [1]. RiPP natural products are typically encoded in a biosynthetic gene cluster (BGC) and produced following defined biosynthetic rules. Initially, a precursor peptide encompassing a core peptide, a leader part and/or a follower part, is synthesised at the ribosome. Next, distinct maturases

Mining raw plant transcriptomic data for new cyclopeptide alkaloids

• Draco Kriger,
• Michael A. Pasquale,
• Brigitte G. Ampolini and
• Jonathan R. Chekan

Beilstein J. Org. Chem. 2024, 20, 1548–1559, doi:10.3762/bjoc.20.138

• the location of the biosynthetic gene cluster (BGC) on the chromosome between base pairs 8,210,000 and 8,480,000. The BGC contained precursor peptides with the core FFFY (gjaA1), FLFY (gjaA2), and FLLY (gjaA3), three potential methyltransferases, and two complete burpitide cyclases all within 266,286

• base pairs (Figure 6B). While the proposed gene cluster is missing a potential peptidase, it contains all the other proteins necessary for the biosynthesis of GJA649 and the other putative G. jasminoides cyclopeptide alkaloids. New cyclopeptide alkaloids in Alternanthera bettzickiana Based on the

• , blue arrows – HMBC. Peptide modifications are shown in purple. A) Precursor peptide sequences found in the transcriptome of G. jasminoides containing the cores FFFY, IFLY, and LFLY. A) GJA649 gene cluster from G. jasminoides. Core sequences from the putative precursor peptides map to three predicted

Computation-guided scaffold exploration of 2E,6E-1,10-trans/cis-eunicellanes

• Zining Li,
• Sana Jindani,
• Volga Kojasoy,
• Teresa Ortega,
• Erin M. Marshall,
• Khalil A. Abboud,
• Sandra Loesgen,
• Dean J. Tantillo and
• Jeffrey D. Rudolf

Beilstein J. Org. Chem. 2024, 20, 1320–1326, doi:10.3762/bjoc.20.115

• never isolated, gave a similar estimated C2–C7 distance of 3.57 Å, suggesting that a factor other than distance controls any subsequent or concomitant cyclization. Cope rearrangement is facile for trans-eunicellanes During our study of the albireticulene (2) biosynthetic gene cluster, we found that 2

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

• analysis of the alp gene cluster from Streptomyces ambofaciens revealed AlpG as the homolog of JadH. The N-terminal His6-tagged construct of AlpG was expressed and purified to homogeneity in E. coli (Figure S2, Supporting Information File 1). The purified AlpG displayed a light yellow color, and the

• biosynthesis of fluostatins involves analogous B-ring cleavage and contraction steps as observed in kinamycin biosynthesis [2][13][19][26]. A sequence analysis of a reported fluostatin biosynthetic gene cluster in reassembled environmental DNA identified Flu17 as the putative ring opening oxygenase [8]. The N

Enhancing structural diversity of terpenoids by multisubstrate terpene synthases

• Min Li and
• Hui Tao

Beilstein J. Org. Chem. 2024, 20, 959–972, doi:10.3762/bjoc.20.86

• which biosynthetic gene clusters for C16 terpenoids were identified and grouped into four types according to the number of MTs and TSs in the gene cluster [59]. A subset of methyltransferase genes was functionally characterized using engineered yeast, which has an enhanced supply of 4 (strain AM109) [60

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

• biosynthetic gene cluster (BGC) that typically includes three P450s, one class II drimenyl diphosphate synthases (DMS), and one characteristic Nudix hydrolase responsible for the DMTs biosynthesis. Among the three P450s, CavA was the only oxygenase acting on drimenol and versatile in oxidizing C-2 and C-3

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

• secondary metabolism in actinomycetes. The technique known as “heterologous expression”, in which a biosynthetic gene cluster of a secondary metabolite is introduced into another organism, is a useful method for producing silent secondary metabolites (Figure 2a). For example, the cryptic trans

• -acyltransferase polyketide synthase biosynthetic gene cluster sdl (80 kb) from Streptomyces sp. B59 was cloned and transferred into a heterologous host, Streptomyces albus J1074, resulting in the production of a class of polycyclic macrolide shuangdaolides A (1), B, and D and dumulmycin (2) [29]. Furthermore

• , 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

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

• organism shares the same habitat with the predator Myxococcus xanthus that feeds on other bacteria including B. subtilis, and bacillaene is the primary factor conferring B. subtilis cells resistance to predation by M. xanthus [8]. The identification of its biosynthetic gene cluster (bae) revealed that the

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

• similar gene cluster was also found in the genome of Cordyceps indigotica (Figure 2A). In this cluster, one bifunctional TC, which we later defined as CiCPS-PS, was present instead of separate TCs, such as AsCPS and AsPS. Although we could identify similar BGCs containing one bifunctional TCs in the

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

• fatty acyl groups. Furthermore, the variochelin biosynthetic gene cluster was identified through draft genome sequencing and gene knockout experiments. Compounds 1–5 exhibited antimicrobial activities against Gram-negative bacteria, including several soil-isolated plant pathogens. Keywords

• draft genome sequence of the H002 strain identified the variochelin biosynthetic gene cluster (var), which encodes PKS (polyketide synthase) and NRPS (non-ribosomal peptide synthetase) genes. Finally, the siderophores isolated in this study exhibited antibacterial activity against several bacteria

• variochelin biosynthetic gene cluster. Biosynthetic pathway of variochelins Nett et al. reported the variochelin biosynthetic gene cluster (NCBI accession number KT900023) encoded in V. boronicumulans, although it has not yet been experimentally validated. In the draft genome sequence of Variovorax sp. H002

Chemical and biosynthetic potential of Penicillium shentong XL-F41

• Ran Zou,
• Xin Li,
• Xiaochen Chen,
• Yue-Wei Guo and
• Baofu Xu

Beilstein J. Org. Chem. 2024, 20, 597–606, doi:10.3762/bjoc.20.52

• fungal-RiPP-like/T1PKS, 1 betalactone, 1 PKS type I/NRPS/indole hybrid, 1 fungal-RiPP-like/T1PKS hybrid, 1 NRP-metallophore/NRPS hybrid, NRPS-like/terpene/phosphonate hybrids, 3 terpenes, and 1 indole-related cluster (Table 5). BGC 7.3, identified as an indole-type gene cluster, includes genes for

• gene cluster for compounds 1 and 2, highlighting ShnA, ShnB, ShnC, ShnD, and ShnE as core genes. B: The diagram proposes biosynthetic pathways for compounds 1 and 2, detailing three potential mechanisms that could convert the five-membered ring structure of compound 2 into the six-membered ring

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

• essential for in vivo antimicrobial activity suggesting a distinct biological function independent of ribosome binding. The hygromycin A biosynthetic gene cluster has been identified and the biosynthesis of the aminocyclitol has been proposed (Figure 1) [8][9]. Starting from glucose-6-phosphate, the pathway

• presence of a resistance gene within a biosynthetic gene cluster can indicate that it produces an antimicrobial compound [27]. We searched for annotated resistance genes in the surrounding genomic neighborhood of PF01408 sequences. We found 1,166 PF01408 sequences were associated with nearby glyoxalase

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

• 2 was determined by Marfey’s method. A biosynthetic gene cluster (BGC) encoding unguisins B and J was compared to characterized BGCs in other Aspergillus sp. Since the unguisin family of heptapetides incorporate different amino acid residues at different positions of the peptide, the A and C domains

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

• , Bunkyo-ku, Tokyo 113-8657, Japan 10.3762/bjoc.20.1 Abstract Recently, we identified the biosynthetic gene cluster of avenalumic acid (ava cluster) and revealed its entire biosynthetic pathway, resulting in the discovery of a diazotization-dependent deamination pathway. Genome database analysis revealed

• expression of BGCs combined with promoter swapping is a powerful tool for the discovery of new natural products from rare actinomycetes. Conclusion In summary, we identified a cma gene cluster for p-coumaric acid biosynthesis in the K. albida genome. We demonstrated the following two biosynthetic reactions

Intermediates and shunt products of massiliachelin biosynthesis in Massilia sp. NR 4-1

• Till Steinmetz,
• Blaise Kimbadi Lombe and
• Markus Nett

Beilstein J. Org. Chem. 2023, 19, 909–917, doi:10.3762/bjoc.19.69

• ], the cyclic guanidine alkaloid massinidine [17], and the siderophore massiliachelin [18]. An antiSMASH analysis [19] of the genome of Massilia sp. NR 4-1 revealed the presence of additional biosynthetic gene clusters, including another putative metallophore gene cluster (ACZ75_RS05545–ACZ75_RS06020

• ). Although the architecture of the corresponding locus suggested an involvement in the production of a lipopeptide siderophore, the gene cluster could not be unequivocally associated with a known compound. The assumption that Massilia sp. NR 4-1 synthesizes iron-chelating molecules in addition to

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

• natural product biosynthetic gene clusters. We highlight the genome mining pipelines' current strengths and limitations by contrasting their advantages and disadvantages. Moreover, we introduce two indirect biosynthetic gene cluster identification strategies that complement current workflows. The

• more difficult to identify. In addition, the size of the BGC of interest impacts the predictive power of the algorithms: Extremely small BGCs, harboring only a few genes, are frequently overlooked as they usually do not pass hard-coded thresholds. For instance, the 1.2 kb gene cluster linked to

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

• nature and possess a variety of biological activities. Up to date, only five fusicoccane-type diterpene synthases have been identified. Here, we identify a two-gene biosynthetic gene cluster containing a new fusicoccane-type diterpene synthase gene tadA and an associated cytochrome P450 gene tadB from

• . 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

• nature. To date, only five distinct FC-type DTSs, including fungi-derived PaFS/SdnA/MgMS and bacteria-derived CotB2/CpCS, have been reported (Figure 1) [20][21][22][23][24], implying that there still exists a large enzymatic space remaining to be explored. Herein, we characterize a two-gene cluster from

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

Synthesis of tryptophan-dehydrobutyrine diketopiperazine and biological activity of hangtaimycin and its co-metabolites

• Houchao Xu,
• Anne Wochele,
• Minghe Luo,
• Gregor Schnakenburg,
• Yuhui Sun,
• Heike Brötz-Oesterhelt and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 1159–1165, doi:10.3762/bjoc.18.120

• against Bacillus subtilis [1]. Together with a structural revision from 29Z to 29E configuration and further biological evaluation of its hepatoprotective properties, its biosynthetic gene cluster was recently identified [2]. The biosynthetic machinery is composed of a hybrid trans-acyltransferase (trans

• supported by bioinformatic analysis of its biosynthetic gene cluster [2], although it seems reasonable to consider 4 as a degradation product of 1. Moreover, the originally reported optical rotation of 4 is positive ([α]D24.5 = +10.0, c 1.1, 95% EtOH [9]), in contrast to the later reported negative value

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

• the N-acyl intermediate for azoxy bonds, suggesting that a genetic region containing both genes could be a potential biosynthetic gene cluster of aliphatic azoxy natural products. Results and Discussion Reactivity-based isolation of azodyrecins from two Streptomyces strains During our efforts toward

• Information File 1). This result identified a similar yet distinct type of azodyrecin biosynthetic gene cluster that contains several insertions and inversions, which generally make it challenging to precisely predict its biosynthetic products based solely on genome information (Figure 2). Taken together, the

Isolation and biosynthesis of daturamycins from Streptomyces sp. KIB-H1544

• Yin Chen,
• Jinqiu Ren,
• Ruimin Yang,
• Jie Li,
• Sheng-Xiong Huang and
• Yijun Yan

Beilstein J. Org. Chem. 2022, 18, 1009–1016, doi:10.3762/bjoc.18.101

• structures of new compounds were elucidated via a joint use of spectroscopic analyses and single-crystal X-ray diffractions. Compounds 1 and 2 belong to a rare class of tricyclic 6/5/6 diarylcyclopentenones, and compounds 3–6 possess a C-18 tricyclic aromatic skeleton. The biosynthetic gene cluster of

• other compounds. To explore the biosynthesis of daturamycins in S. sp. KIB-H1544, especially the formation mechanism of the tricyclic 6/5/6 scaffold, the biosynthetic gene cluster of daturamycins was found and confirmed by gene knockout experiments. We also characterized the deduced peptide synthetase

• -epoxide hydrolase), which share high sequence similarity with the echoside (Figure 1) biosynthetic gene cluster [26] (EchA, 69.2% identity to DatA; EchB, 78.9% identity to DatB; EchC, 66.9% identity to DatC) (Figure 3A). Additionally, one bilirubin oxidase (DatD) and NADPH-dependent oxidoreductase (DatE

Efficient production of clerodane and ent-kaurane diterpenes through truncated artificial pathways in Escherichia coli

• Fang-Ru Li,
• Xiaoxu Lin,
• Qian Yang,
• Ning-Hua Tan and
• Liao-Bin Dong

Beilstein J. Org. Chem. 2022, 18, 881–888, doi:10.3762/bjoc.18.89

• ) (Table S4, Supporting Information File 1). Additionally, a GGDP synthase named GGDPS was also successfully cloned from the same strain. These results suggested that K. griseola DSM 43859 is a different strain with K. griseolosporeus MF730-N6 and likely includes a similar biosynthetic gene cluster in the

Identification of the new prenyltransferase Ubi-297 from marine bacteria and elucidation of its substrate specificity

• Jamshid Amiri Moghaddam,
• Huijuan Guo,
• Karsten Willing,
• Thomas Wichard and
• Christine Beemelmanns

Beilstein J. Org. Chem. 2022, 18, 722–731, doi:10.3762/bjoc.18.72

• EboA-E have not been investigated yet in detail. The wide spread occurrence of the ebo gene cluster region within genomes of bacterial symbionts associated, e.g., with marine algae, such as Maribacter sp. MS6 [29][30][31], sparked our interest. To provide more insights into the structural basis of UbiA