Publications

2023

[100] Schwitalla, J. W., Le, N.-T. H., et al. Heterologous expression of the cryptic mdk gene cluster and structural revision of maduralactomycin A. RSC Advances, 2023, 13, 34136 - 34144. https://doi.org/10.1039/D3RA05931F

Abstract

After conducting an in silico analysis of the cryptic mdk cluster region and performing transcriptomic studies, an integrative Streptomyces BAC Vector containing the mdk gene sequence was constructed. The heterologous expression of the mdk cluster in Streptomyces albus J1074 resulted in the production of the angucyclic product, seongomycin, which allowed for the assesment of its antibacterial, antiproliferative, and antiviral activities. Heterologous production was further confirmed by targeted knock-out experiments involving key regulators of the biosynthetic pathways. We were further able to revise the core structure of maduralactomycin A, using a computational approach.

[99] Seibel, E., Um, S., Dayras, M. et al. Genome mining for macrolactam-encoding gene clusters allowed for the network-guided isolation of β-amino acid-containing cyclic derivatives and heterologous production of ciromicin A. Commun Chem 6, 257 (2023). https://doi.org/10.1038/s42004-023-01034-w

Abstract

β-Amino acid-containing macrolactams represent a structurally diverse group of bioactive natural products derived from polyketides; however we are currently lacking a comprehensive overview about their abundance across bacterial families and the underlying biosynthetic diversity. In this study, we employed a targeted β-amino acid-specific homology-based multi-query search to identify potential bacterial macrolactam producers. Here we demonstrate that approximately 10% of each of the identified actinobacterial genera harbor a biosynthetic gene cluster (BGC) encoding macrolactam production. Based on our comparative study, we propose that mutations occurring in specific regions of polyketide synthases (PKS) are the primary drivers behind the variation in macrolactam ring sizes. We successfully validated two producers of ciromicin A from the genus Amycolatopsis, revised the composition of the biosynthetic gene cluster region mte of macrotermycins, and confirmed the ciromicin biosynthetic pathway through heterologous expression. Additionally, network-based metabolomic analysis uncovered three previously unreported macrotermycin congeners from Amycolatopsis sp. M39. The combination of targeted mining and network-based analysis serves as a powerful tool for identifying macrolactam producers and our studies will catalyze the future discovery of yet unreported macrolactams.

[98] Kreuzenbeck, N.B., Dhiman, S., Roman, D. et al. Isolation, (bio)synthetic studies and evaluation of antimicrobial properties of drimenol-type sesquiterpenes of Termitomyces fungi. Commun Chem 6, 79 (2023). https://doi.org/10.1038/s42004-023-00871-z

Abstract

Macrotermitinae termites have farmed fungi in the genus Termitomyces as a food source for millions of years. However, the biochemical mechanisms orchestrating this mutualistic relationship are largely unknown. To deduce fungal signals and ecological patterns that relate to the stability of this symbiosis, we explored the volatile organic compound (VOC) repertoire of Termitomyces from Macrotermes natalensis colonies. Results show that mushrooms emit a VOC pattern that differs from mycelium grown in fungal gardens and laboratory cultures. The abundance of sesquiterpenoids from mushrooms allowed targeted isolation of five drimane sesquiterpenes from plate cultivations. The total synthesis of one of these, drimenol, and related drimanes assisted in structural and comparative analysis of volatile organic compounds (VOCs) and antimicrobial activity testing. Enzyme candidates putatively involved in terpene biosynthesis were heterologously expressed and while these were not involved in the biosynthesis of the complete drimane skeleton, they catalyzed the formation of two structurally related monocyclic sesquiterpenes named nectrianolins.

[97] Albert T. H. Bartholomäus, Dávid Roman, Walid K. Al-Jammal, Prof. Dr. Ivan Vilotijević, Prof. Dr. Christine Beemelmann Synthesis of Aryl- and Alkyl-Containing 3-Methylene-5-hydroxy Esters via a Barbier Allylation Reaction EurJOC doi: 10.1002/ejoc.202300177

Abstract

The formation of C−C bonds via the allylation of carbonyl compounds has been widely applied in total syntheses. Amongst the many possible strategies, the Barbier-type allylation in aqueous media has received only moderate attention over the last decades despite its mild reaction conditions. In this study, we investigated the indium (In⁰) and zinc (Zn⁰) mediated Barbier allylation reaction to efficiently synthesize base-labile 3-methylene-5-hydroxy containing building blocks for natural product total synthesis. As model study we selected the allylation of lipidic undecanal with ethyl 3-(bromomethyl)but-3-enoate in the presence of either Zn⁰ or In⁰ and investigated the effects of additives on yields and selectivities. We then applied the optimized reaction conditions to sterically demanding allyl bromides and functionalized aromatic aldehydes yielding eleven new homoallylic alcohols, one of which was further transformed via oxidation and reduction sequences.

[96] Bodawatta KH, Hu H, Schalk F, Daniel JM, Maiah G, Koane B, Iova B, Beemelmanns C, Poulsen M, Jønsson KA. Multiple mutations in the Nav1.4 sodium channel of New Guinean toxic birds provide autoresistance to deadly batrachotoxin. Mol Ecol. 2023. doi: 10.1111/mec.16878.

Abstract

We examine genomic adaptations that could facilitate autoresistance to the diet-acquired potent neurotoxic alkaloid batrachotoxin (BTX) in New Guinean toxic birds. Our work documents two new toxic bird species and shows that toxic birds carry multiple mutations in the SCN4A gene that are under positive selection. This gene encodes the most common vertebrate muscle Nav channel (Nav1.4). Molecular docking results indicate that some of the mutations that are present in the pore-forming segment of the Nav channel, where BTX binds, could reduce its binding affinity.

[95] Fricke J, Schalk F, Kreuzenbeck NB, Seibel E, Hoffmann J, Dittmann G, Conlon BH, Guo H, Wilhelm de Beer Z, Vassão DG, Gleixner G, Poulsen M, Beemelmanns C. Adaptations of Pseudoxylaria towards a comb-associated lifestyle in fungus-farming termite colonies. ISME J. 2023, doi: 10.1038/s41396-023-01374-4.

Abstract

Capitalizing on viable Pseudoxylaria cultures from different termite colonies, we obtained genomes of seven and transcriptomes of two Pseudoxylaria isolates. Using a whole-genome-based comparison with free-living members of the genus Xylaria, we document that the association has been accompanied by significant reductions in genome size, protein-coding gene content, and reduced functional capacities related to oxidative lignin degradation, oxidative stress responses and secondary metabolite production. Functional studies based on growth assays and fungus-fungus co-cultivations, coupled with isotope fractionation analysis, showed that Pseudoxylaria only moderately antagonizes growth of the termite food fungus Termitomyces, and instead extracts nutrients from the food fungus biomass for its own growth

2022

[94] Guo H, Daniel JM, Seibel E, Burkhardt I, Conlon BH, Görls H, Vassão DG, Dickschat JS, Poulsen M, Beemelmanns C* (2022). Insights into the Metabolomic Capacity of Podaxis and Isolation of Podaxisterols A-D, Ergosterol Derivatives Carrying Nitrosyl Cyanide-Derived Modifications. J Nat Prod, 85(9), 2159-2167.

[93] Raguž L,^# Peng CC,^# Rutaganira FUN, Krüger T, Stanisic A, Jautzus T, Kries H, Kniemeyer O, Brakhage A, King N, Beemelmanns C* (2022). Total synthesis and functional evaluation of IORs, sulfonolipid-based inhibitors of cell differentiation in Salpingoeca rosetta. Angew Chem Int Ed, e202209105.

Abstract

A new and modular synthesis of the rosette-inhibitor sulfonolipid IOR-1A and chemical probes was achieved via decarboxylative cross-coupling reaction of a desymmetrized tartaric acid derivatives and alkyl zinc reagents of choice. Synthesized congeners and bifunctional probes allowed to determine structure-activity relation to profile binding partners in producer and recipient for the first time.

[92] Hoefgen S, Bissell AU, Huang Y, Gherlone F, Raguž L, Beemelmanns C, Valiante V (2022). Desaturation of the sphingofungin polyketide tail results in increased serine palmitoyltransferase inhibition. Microbiol Spectr, e0133122.

Abstract

Sphingofungins belong to a group of structurally related sphingolipid inhibitors produced by fungi, which specifically inhibit serine palmitoyl transferases, enzymes catalyzing the initial step during sphingolipid biosynthesis. We identified and elucidated the biosynthetic gene cluster responsible for the biosynthesis of sphingofungins B, C, and D in Aspergillus fumigatus. In vitro analyses have shown that sphingofungin biosynthesis starts with the condensation of a C18 polyketide with the uncommon substrate aminomalonate.

[91] Guo H,* Rischer M, Beemelmanns C* (2022). Signalling molecules inducing metamorphosis in marine organisms. Nat Prod Rep 39(9), 1833-1855 (Review).

Abstract

Covering: findings from early 1980s until early 2022Microbial-derived cues of marine biofilms induce settlement and metamorphosis of marine organisms, a process responsible for the emergence of diverse flora and fauna in marine habitats. Although this phenomenon is known for more than 80 years, the research field has only recently gained much momentum. Here, we summarize the currently existing biochemical and microbial knowledge about microbial signalling molecules, con-specific signals, and synthetic compounds that induce or prevent recruitment, settlement, and metamorphosis in invertebrate larvae. We discuss the possible modes of action and conclude with perspectives for future research directions in the field of marine chemical ecology.

[90] Bissell AU, Rautschek J, Hoefgen S, Raguž L, Mattern DJ, Saeed N, Janevska S, Jojić K, Huang Y, Kufs JE, Herboeck B, Guo H, Hillmann F, Beemelmanns C, Valiante V (2022). Biosynthesis of the Sphingolipid inhibitors Sphingofungins in filamentous fungi requires aminomalonate as a metabolic precursor. ACS Chem Biol 17(2), 386-394.

Abstract

Serine palmitoyltransferase catalyzes the first step of the sphingolipid biosynthesis. Recently, sphingolipid homeostasis has been connected to several human diseases, making serine palmitoyltransferases an interesting therapeutic target. Known and efficient serine palmitoyltransferase-inhibitors are sphingofungins, a group of natural products isolated from fungi. To further characterize newly isolated sphingofungins, we designed an easy to use colorimetric serine palmitoyltransferase activity assay using FadD, which can be performed in 96-well plates. Because sphingofungins exert antifungal activitiy as well, we compared the in vitro assay results with an in vivo growth assay using Saccharomyces cerevisiae. The reported experiments showed differences among the assayed sphingofungins, highlighting an increase of activity based on the saturation levels of the polyketide tail.

[89] Grosse M, Günther K, Jordan PM, Roman D, Werz O, Beemelmanns C* (2022). Synthesis of functionalized δ-hydroxy-β-keto esters and evaluation of their anti-inflammatory properties. Chembiochem 23(9), e202200073.

Abstract

Synthesis of functionalized δ-hydroxy-β-keto esters using Chan's diene and modified Mukaiyama-aldol reaction conditions. Diastereoselective reduction to syn- and anti-diols and saponification yielded the respective acids. All synthesized compounds were evaluated for their 5-lipoxygenase activity.

[88] Kreuzenbeck NB, Seibel E, Schwitalla JW, Fricke J, Conlon BH, Schmidt S, Hammerbacher A, Köllner TG, Poulsen M, Hoffmeister D, Beemelmanns C* (2022). Comparative genomic and metabolomic analysis of Termitomyces species provides insights into the terpenome of the fungal cultivar and the characteristic odor of the fungus garden of Macrotermes natalensis termites. mSystems 7(1), e0121421.

Abstract

We determined the typical volatile emission of fungus comb biomass and Termitomyces nodules, revealing α-pinene, camphene, and d-limonene as the most abundant terpenes. Genome mining of Termitomyces followed by gene expression studies and phylogenetic analysis of putative enzymes related to secondary metabolite production encoded by the genomes uncovered a conserved and specific biosynthetic repertoire across strains. Finally, we proved by heterologous expression and in vitro enzymatic assays that a highly expressed gene sequence encodes a rare bifunctional mono-/sesquiterpene cyclase able to produce the abundant comb volatiles camphene and d-limonene.

[87] Lee SR, Schalk F, Schwitalla JW, Guo H, Yu JS, Song M, Jung WH, de Beer ZW, Beemelmanns C*, Kim KH* (2022). GNPS**-guided discovery of madurastatins A1, A2, E1, F, and G1, siderophores from the termite-associated Actinomadura sp. RB99. Chemistry 28(36), e202200612.

Abstract

Metabolomic analysis of cocultures of Actinomadura sp. RB99 with fungal symbionts of termites allowed for the MS-guided isolation of four unreported madurastatin derivatives, including a siderophore-metal complex thereof.

[86] Moghaddam Amri J, Guo H, Willing K, Wichard T, Beemelmanns C* (2022). Identification of the new prenyltransferase Ubi-297 from marine bacteria and elucidation of its substrate specificity, Beilstein J. Org. Chem (18), 722-731.

Abstract

Aromatic prenylated metabolites have important biological roles and activities in all living organisms. Compared to their importance in all domains of life, we know relatively little about their substrate scopes and metabolic functions. Here, we describe a new UbiA-like prenyltransferase (Ptase) Ubi-297 encoded in a conserved operon of several bacterial taxa, including marine Flavobacteria and the genus Sacchromonospora. In silico analysis of Ubi-297 homologs indicated that members of this Ptase group are composed of several transmembrane α-helices and carry a conserved and distinct aspartic-rich Mg2+-binding domain. We heterologously produced UbiA-like Ptases from the bacterial genera Maribacter, Zobellia, and Algoriphagus in Escherichia coli. Investigation of their substrate scope uncovered the preferential farnesylation of quinoline derivatives, such as 8-hydroxyquinoline-2-carboxylic acid (8-HQA) and quinaldic acid. The results of this study provide new insights into the abundance and diversity of Ptases in marine Flavobacteria and beyond.

[85] Sauer M, Beemelmanns C* (2022). Application of pyrrolo-protected amino aldehydes in the stereoselective synthesis of anti 1,2-amino alcohols. ChemCom 58(64), 8990-8993.

Abstract

Herein, we demonstrate the applicability of the 2,5-dimethylpyrrolo unit as a complementary N-protecting group in the highly diastereoselective synthesis of more than 20 different anti-amino alcohols (63–90% yields with up to 20 : 1 dr). Cleavage of the pyrrolo-N-protecting group was accomplished, e.g. in the presence of NH2OH under microwave conditions with yields exceeding 80%. The applicability of the protecting groups was further demonstrated by a short total synthesis of the sphinganine-like natural product clavaminol A. The introduction of the N-pyrrolo protecting group also offers the possibility to analyse product mixtures by NMR measurements due to the absence of conformational isomers, which are otherwise common for N-protecting groups.

[84] Raguž L, Peng CC, Kaiser M, Görls H, Beemelmanns C^* (2022). A modular approach to the antifungal Sphingofungin family: Concise total synthesis of Sphingofungin A and C. Angew Chem Int Ed, e202112616.

Abstract

Sphingofungins are fungal natural products known to inhibit the biosynthesis of sphingolipids which play pivotal roles in various cell functions. Here, we report a short and flexible synthetic approach towards the sphingofungin family. Key step of the synthesis was a decarboxylative cross-coupling reaction of chiral sulfinyl imines with a functionalized tartaric acid derivative, which yielded the core motif of sphingofungins carrying four consecutive stereocenters and a terminal double bond. Subsequent metathesis reaction allowed for the introduction of different side chains of choice resulting in a total of eight sphingofungins, including for the first time sphingofungin C (eight steps from commercially available protected tartaric acid with an overall yield of 6 %) and sphingofungin A (ten steps). All newly synthesized derivatives were tested for their antifungal, cell-proliferative and antiparasitic activity unraveling their structure–activity relations.

2021

[83] Amiri Moghaddam J, Jautzus T, Alanjary M, Beemelmanns C* (2021). Recent highlights of biosynthetic studies on marine natural products. Org Biomol Chem 19(1), 123-140. (Review)

[82] Conlon BH, Gostinčar C, Fricke J, Kreuzenbeck NB, Daniel JM, Schlosser MSL, Peereboom N, Aanen DK, de Beer ZW, Beemelmanns C, Gunde-Cimerman N, Poulsen M (2021). Genome reduction and relaxed selection is associated with the transition to symbiosis in the basidiomycete genus Podaxis. iScience 24(6), 102680.

[81] Guo H, Rischer M, Westermann M, Beemelmanns C* (2021). Two distinct bacterial biofilm components trigger metamorphosis in the colonial hydrozoan Hydractinia echinata. mBio 12(3), e0040121.

[80] Lee SR, Guo H, Yu JS, Park M, Dahse HM, Jung WH, Beemelmanns C*, Kim KH* (2021). Revised structural assignment of azalomycins based on genomic and chemical analysis. Org Chem Front 8, 4791-4798.

[79] Leichnitz D, Peng CC, Raguž L, Rutaganira FUN, Jautzus T, Regestein L, King N, Beemelmanns C* (2021). Structural and functional analysis of bacterial sulfonosphingolipids and rosette-inducing factor 2 (RIF-2) by mass spectrometry-guided isolation and total synthesis. Chemistry, 28(8), e202103883.

[78] Loos D^*, Zhang L, Beemelmanns C, Kurzai O, Panagiotou G* (2021). DAnIEL: A user-friendly web server for fungal ITS amplicon sequencing data. Front Microbiol 12, 720513.

^*corresponding author, # equal contribution