Collimonins A–D, Unstable Polyynes with Antifungal or Pigmentation Activities from the Fungus-Feeding Bacterium Collimonas fungivorans Ter331

Advanced crystallography for structure determination of natural products

Covering: up to 2025Crystallographic analysis has become the most reliable method for elucidating the structures of natural products, as it can provide absolute configurations with precise spatial arrangement information at the molecular level. However, obtaining high-quality and suitable-sized single crystals can be challenging for many natural products, making their structure determination difficult through traditional crystallography techniques. Recent advancements in this field have introduced innovative strategies to overcome the obstacle. These cutting-edge strategies include post-orientation of organic molecules within pre-prepared porous crystals (crystalline sponge method), co-crystallization of organic molecules with a crystalline mate through supramolecular interactions (crystalline mate method), encapsulation of organic molecules within inert oil nanodroplets (encapsulated nanodroplet crystallization method), and the use of electron diffraction and microscopy for nanocrystals (microcrystal electron diffraction method). This highlight delves into the fundamental principles, key characteristics, and representative applications of each strategy, as well as their respective advantages and limitations, aiming to guide researchers in choosing the most suitable crystallography approach for analyzing the structures of natural products.

Bacterial polyynes uncovered: a journey through their bioactive properties, biosynthetic mechanisms, and sustainable production strategies

Covering: up to 2023Conjugated polyynes are natural compounds characterized by alternating single and triple carbon-carbon bonds, endowing them with distinct physicochemical traits and a range of biological activities. While traditionally sourced mainly from plants, recent investigations have revealed many compounds originating from bacterial strains. This review synthesizes current research on bacterial-derived conjugated polyynes, delving into their biosynthetic routes, underscoring the variety in their molecular structures, and examining their potential applications in biotechnology. Additionally, we outline future directions for metabolic and protein engineering to establish more robust and stable platforms for their production.

A Burkholderia cenocepacia-like environmental isolate strongly inhibits the plant fungal pathogen Zymoseptoria tritici

Fungal phytopathogens cause significant reductions in agricultural yields annually, and overusing chemical fungicides for their control leads to environmental pollution and the emergence of resistant pathogens. Exploring natural isolates with strong antagonistic effects against pathogens can improve our understanding of their ecology and develop new treatments for the future. We isolated and characterized a novel bacterial strain associated with the species Burkholderia cenocepacia, termed APO9, which strongly inhibits Zymoseptoria tritici, a commercially important pathogenic fungus causing Septoria tritici blotch in wheat. Additionally, this strain exhibits inhibitory activity against four other phytopathogens. We found that physical contact plays a crucial role for APO9's antagonistic capacity. Genome sequencing of APO9 and biosynthetic gene cluster (BGC) analysis identified nine classes of BGCs and three types of secretion systems (types II, III, and IV), which may be involved in the inhibition of Z. tritici and other pathogens. To identify genes driving APO9's inhibitory activity, we screened a library containing 1,602 transposon mutants and identified five genes whose inactivation reduced inhibition efficiency. One such gene encodes for a diaminopimelate decarboxylase located in a terpenoid biosynthesis gene cluster. Phylogenetic analysis revealed that while some of these genes are also found across the Burkholderia genus, as well as in other Betaproteobacteria, the combination of these genes is unique to the Burkholderia cepacia complex. These findings suggest that the inhibitory capacity of APO9 is complex and not limited to a single mechanism, and may play a role in the interaction between various Burkholderia species and various phytopathogens within diverse plant ecosystems.

IMPORTANCE

The detrimental effects of fungal pathogens on crop yields are substantial. The overuse of chemical fungicides contributes not only to environmental pollution but also to the emergence of resistant pathogens. Investigating natural isolates with strong antagonistic effects against pathogens can improve our understanding of their ecology and develop new treatments for the future. We discovered and examined a unique bacterial strain that demonstrates significant inhibitory activity against several phytopathogens. Our research demonstrates that this strain has a wide spectrum of inhibitory actions against plant pathogens, functioning through a complex mechanism. This plays a vital role in the interactions between plant microbiota and phytopathogens.

Disproof of the Structures and Biosynthesis of Ergoynes, Gs-Polyyne-l-Ergothioneine Cycloadducts from Gynuella sunshinyii YC6258

Some bacteria produce "bacterial polyynes" bearing a conjugated C≡C bond that starts with a terminal alkyne. Ergoynes A and B have been reported as sulfur-containing metabolites from Gynuella sunshinyii YC6258. These compounds were thought to be formed by cycloaddition between a bacterial polyyne (named Gs-polyyne) and l-ergothioneine. The biosynthetic gene clusters (BGCs), which may contribute to their synthesis, were present in the YC6258 genome. The biosynthetic origin of Gs-polyyne is interesting considering its rare 2-isopentyl fatty acyl skeleton. Here, the structures and biosynthesis of Gs-polyyne and ergoynes were verified by analytical, chemical, and genetic techniques. In the YC6258 extract, which was prepared considering their instability, Gs-polyyne was detected as a major LC peak, and ergoynes were not detected. The NMR data of the isolated Gs-polyyne contradicted the proposed structure and identified it as the previously reported protegenin A. The expression of Gs-polyyne BGC in Escherichia coli BL21(DE3) also yielded protegenin A. The cyclization between protegenin A and l-ergothioneine did not proceed during sample preparation; a base, such as potassium carbonate, was required. Overall, Gs-polyyne was identified as protegenin A, while ergoynes were determined to be artifacts. This cyclization may provide a derivatization to stabilize polyynes or create new chemical space.

Structures and Biosynthesis of Caryoynencins, Unstable Bacterial Polyynes from Pseudomonas protegens Recombinant Expressing the cayG Gene

Bacteria in certain genera can produce "bacterial polyynes" that contain a conjugated C≡C bond starting from a terminal alkyne. Protegenin A is a derivative of octadecanoic acid that contains an ene-tetrayne moiety. It was discovered in Pseudomonas protegens Cab57 and exhibits strong antioomycete and moderate antifungal activity. By introducing cayG, a cytochrome P450 gene from Burkholderia caryophylli, into P. protegens Cab57, protegenin A was converted into more complex polyynes, caryoynencins A-E. A purification method that minimized the degradation and isomerization of caryoynencins was established. For the first time, as far as we know, the 1H and 13C{1H} NMR signals of caryoynencins were completely assigned by analyzing the NMR data of the isolated compounds and protegenin A enriched with [1-13C]- or [2-13C]-acetate. Through the structural analysis of caryoynencins D/E and bioconversion experiments, we observed that CayG constructs the allyl alcohol moiety of caryoynencins A-C through sequential hydroxylation, dehydration, and hydroxylation. The recombinant strain exhibited a stronger antioomycete activity compared to the wild-type strain. This paper proposes a stable purification and structural determination method for various bacterial polyynes, and P. protegens Cab57 holds promise as an engineering host for the production of biologically active polyynes.

Genome-based analyses of family Oxalobacteraceae reveal the taxonomic classification

Family Oxalobacteraceae is known for the indicator of bacterial diversity in the environment and many of which are important beneficial bacteria. Previous studies on the taxonomic structure of family Oxalobacteraceae mostly relied on 16S rRNA gene analysis, or core-genome phylogeny of a limited number of species and resulted in taxonomic confusion within several genera. Developments in sequencing technologies have allowed more genome sequences to be obtained, enabling the revision of family Oxalobacteraceae. Here, we report a comprehensive analysis of phylogenomic trees, concatenated protein and up-to-date bacterial core gene phylogenetic trees, and genomic metrics for genus demarcation on 135 genomes of Oxalobacteraceae species to elucidate their interrelationships. Following this framework for classification of species in family Oxalobacteraceae, all the proposed genera formed monophyletic lineages in the phylogenomic trees and could also be clearly separated from others in the genomic similarity indexes of average amino acid identity, percentage of conserved proteins and core-proteome average amino acid identity.

Polyyne-producing Burkholderia suppress Globisporangium ultimum damping-off disease of Pisum sativum (pea)

Extensive crop losses are caused by oomycete and fungal damping-off diseases. Agriculture relies heavily on chemical pesticides to control disease, but due to safety concerns multiple agents have been withdrawn. Burkholderia were successfully used as commercial biopesticides because of their fungicidal activity and plant protective traits. However, their potential for opportunistic pathogenicity led to a moratorium on their registration as biopesticides. Subsequently, Burkholderia were shown to produce multiple specialised metabolites including potent antimicrobial polyynes. Cepacin A, a polyyne produced by Burkholderia ambifaria biopesticide strains was shown to be an important metabolite for the protection of germinating peas against Globisporangium ultimum (formerly Pythium) damping-off disease. Recently, there has been an expansion in bacterial polyyne discovery, with the metabolites and their biosynthetic gene pathways found in several bacterial genera including Burkholderia, Collimonas, Trinickia, and Pseudomonas. To define the efficacy of these bacterial polyyne producers as biopesticidal agents, we systematically evaluated metabolite production, in vitro microbial antagonism, and G. ultimum biocontrol across a panel of 30 strains representing four bacterial genera. In vitro polyyne production and antimicrobial activity was demonstrated for most strains, but only Burkholderia polyyne producers were protective within the in vivo G. ultimum damping-off pea protection model. B. ambifaria was the most effective cepacin-expressing biopesticide, and despite their known potential for plant pathogenicity Burkholderia gladioli and Burkholderia plantarii were uniquely shown to be protective as caryoynencin-producing biopesticides. In summary, Burkholderia are effective biopesticides due to their suite of antimicrobials, but the ability to deploy polyyne metabolites, caryoynencin and cepacin, is strain and species dependent. Graphical Abstract.

Genome Mining Discovery of Protegenins A-D, Bacterial Polyynes Involved in the Antioomycete and Biocontrol Activities of Pseudomonas protegens

Some bacteria uniquely produce "bacterial polyynes", which possess a conjugated C≡C bond starting with a terminal alkyne, and use them as chemical weapons against hosts and competitors. Pseudomonas protegens Cab57, a biocontrol agent against plant pathogens, has an orphan biosynthetic gene cluster for bacterial polyynes (named protegenins). In this study, the isolation, structure elucidation, and biological characterization of protegenins A-D are reported. The structures of protegenins A-D determined by spectroscopic and chemical techniques were octadecanoic acid derivatives possessing an ene-tetrayne, ene-triyne-ene, or ene-triyne moiety. The protegenins exhibited weak to strong antioomycete activity against Pythium ultimum OPU774. The deletion of proA, a protegenin biosynthetic gene, resulted in the reduction of the antioomycete activity of P. protegens. The Gac/Rsm system, a quorum sensing-like system of Pseudomonas bacteria, regulated the production of protegenins. The production profile of protegenins was dependent on the culturing conditions, suggesting a control mechanism for protegenin production selectivity. P. protegens suppressed the damping-off of cucumber seedlings caused by P. ultimum, and this protective effect was reduced in the proA-deletion mutant. Altogether, protegenins are a new class of bacterial polyynes which contribute to the antioomycete and plant-protective effects of P. protegens.

Effects of Structural Variations on Antibacterial Properties for Conjugated Diynes Generated through Glaser Hay Couplings

Antibiotic resistance is a growing problem facing global societies today. Many new antibiotics are derivatized versions of already existing antibiotics, which allows for antibiotic resistance to arise. To combat this issue, new antibiotics with different core structures need to be elucidated. Asymmetrical polyacetylenes have been isolated from natural products and they have previously been demonstrated to exhibit antimicrobial and antibacterial activity; however, their synthetic preparation has not made them easily amenable to rapid derivatization for SAR studies. Using a combination of solution and solid-supported chemistries, an array of diynes inspired by a known natural product were prepared and assessed for antibacterial activity. Ultimately, several compounds were identified with improved activity in bacterial viability assays. Moreover, some compounds were discovered that displayed a degree of specificity for E. coli over P. fluorescens and vice versa. These new compounds show promise, and further investigation is needed to pinpoint the specific structural components that elicit biological activity.

Thiotemplated Biosynthesis of Bacterial Polyyne Fatty Acids by a Designated Desaturase Triad

Various bacterial species are capable of producing highly modified fatty acid derivatives with conjugated triple bonds, which play important ecological roles as antifungals and toxins in mutualistic and pathogenic interactions. Furthermore, the terminal polyyne moiety is of interest as pharmacophore and as tag in bioorthogonal chemistry and live imaging. To gain insight into the assembly of these highly reactive natural products, we investigated tetrayne (caryoynencin and protegencin) biosynthesis genes (cay and pgn) from Trinickia caryophylli and Pseudomonas protegens. Pathway dissection and reconstitution in the heterologous host Burkholderia graminis revealed the genes minimally required for polyyne formation. Mutational analyses and biochemical assays demonstrated that polyyne biosynthesis is thiotemplated, involving a fatty acyl-AMP ligase, a designated acyl carrier protein, and a thioesterase. Heterologous expression of point-mutated desaturase genes showed that three desaturases work synergistically to introduce four triple bonds. These findings point to an intricate desaturase complex and provide important information for future bioengineering experiments.

Sequential Allylic Alcohol Formation by a Multifunctional Cytochrome P450 Monooxygenase with Rare Redox Partners

Caryoynencin is a toxic and antifungal fatty acid derivative produced by a number of plant-pathogenic and insect-protective bacteria (Trinickia caryophylli and Burkholderia spp.). In addition to the reactive tetrayne unit, the presence of an allylic alcohol moiety is critical for antimicrobial activities. By a combination of mutational analyses, heterologous expression and in vitro reconstitution experiments we show that the cytochrome P450 monooxygenase CayG catalyzes the complex transformation of a saturated carbon backbone into an allylic alcohol. Unexpectedly, CayG employs a ferritin-like protein (CayK) or a rubredoxin (CayL) component for electron transport. A desaturation-hydroxylation sequence was deduced from a time-course study and in vitro biotransformations with pathway intermediates, substrate analogues, protegencin congeners from Pseudomonas protegens Pf-5, and synthetic derivatives. This unusual multifunctional oxygenase may inspire future biocatalytic applications.

Biosynthesis of Isonitrile- and Alkyne-Containing Natural Products

Natural products are a diverse class of biologically produced compounds that participate in fundamental biological processes such as cell signaling, nutrient acquisition, and interference competition. Unique triple-bond functionalities like isonitriles and alkynes often drive bioactivity and may serve as indicators of novel chemical logic and enzymatic machinery. Yet, the biosynthetic underpinnings of these groups remain only partially understood, constraining the opportunity to rationally engineer biomolecules with these functionalities for applications in pharmaceuticals, bioorthogonal chemistry, and other value-added chemical processes. Here, we focus our review on characterized biosynthetic pathways for isonitrile and alkyne functionalities, their bioorthogonal transformations, and prospects for engineering their biosynthetic machinery for biotechnological applications.

Integrated omics approach to unveil antifungal bacterial polyynes as acetyl-CoA acetyltransferase inhibitors

Bacterial polyynes are highly active natural products with a broad spectrum of antimicrobial activities. However, their detailed mechanism of action remains unclear. By integrating comparative genomics, transcriptomics, functional genetics, and metabolomics analysis, we identified a unique polyyne resistance gene, masL (encoding acetyl-CoA acetyltransferase), in the biosynthesis gene cluster of antifungal polyynes (massilin A 1, massilin B 2, collimonin C 3, and collimonin D 4) of Massilia sp. YMA4. Crystallographic analysis indicated that bacterial polyynes serve as covalent inhibitors of acetyl-CoA acetyltransferase. Moreover, we confirmed that the bacterial polyynes disrupted cell membrane integrity and inhibited the cell viability of Candida albicans by targeting ERG10, the homolog of MasL. Thus, this study demonstrated that acetyl-CoA acetyltransferase is a potential target for developing antifungal agents.

In a multi-omics analysis, bacterial polyynes are found to act as antifungal agents by inhibiting the Candida albicans polyyne resistance gene ERG10, the homolog of MasL encoding acetyl-CoA acetyltransferase.

Microbiome and related structural features of Earth's most archaic plant indicate early plant symbiosis attributes

Origin of earliest land plants from ancestral algae dramatically accelerated the evolution of Earth’s terrestrial ecosystems, in which microbial symbioses have played key roles. Recent molecular diversification analyses identify the rare, geographically-limited moss Takakia as Earth’s most archaic modern land plant. Despite occupying a phylogenetic position pivotal for understanding earliest plants, Takakia microbial associations are poorly known. Here, we describe symbiosis-related structural features and contig-based metagenomic data that illuminate the evolutionary transition from streptophyte algae to early embryophytes. We observed that T. lepidozioides shares with streptophyte algae secretion of microbe-harboring mucilage and bacterial taxa such as Rhizobium and genes indicating nitrogen fixation. We find that Takakia root-analogs produce lateral mucilage organs that are more complex than generally understood, having structural analogies to angiosperm lateral roots adapted for N-fixation symbioses, including presence of intracellular microbes. We also find structural and metagenomic evidence for mycorrhiza-like species of glomalean fungi (including Rhizophagus irregularis) not previously known for mosses, as well as ascomycete fungi (e.g. Rhizoscyphus ericae) that associate with other early-diverging plants. Because Takakia is the oldest known modern plant genus, this study of plants of a remote locale not strongly influenced by human activities may indicate microbiome features of early land plants.

Untargeted Identification of Alkyne-Containing Natural Products Using Ruthenium-Catalyzed Azide Alkyne Cycloaddition Reactions Coupled to LC-MS/MS

Alkyne-containing natural products have been identified from plants, insects, algae, fungi, and bacteria. This class of natural products has been characterized as having a variety of biological activities. Polyynes are a subclass of acetylenic natural products that contain conjugated alkynes and are underrepresented in natural product databases due to the fact that they decompose during purification. Here we report a workflow that utilizes alkyne azide cycloaddition (AAC) reactions followed by LC-MS/MS analysis to identify acetylenic natural products. In this report, we demonstrate that alkyne azide cycloaddition reactions with p-bromobenzyl azide result in p-bromobenzyl-substituted triazole products that fragment to a common brominated tropylium ion. We were able to identify a synthetic alkyne spiked into the extract of Anabaena sp. PCC 7120 at a concentration of 10 μg/mL after optimization of MS/MS conditions. We then successfully identified the known natural product fischerellin A in the extract of Fischerella muscicola PCC 9339. Lastly, we identified the recently identified natural products protegenins A and C from Pseudomonas protegens Pf-5 through a combination of genome mining and RuAAC reactions. This is the first report of RuAAC reactions to detect acetylenic natural products. We also compare CuAAC and RuAAC reactions and find that CuAAC reactions produce fewer byproducts compared to RuAAC but is limited to terminal-alkyne-containing compounds. In contrast, RuAAC is capable of identification of both terminal and internal acetylenic natural products, but byproducts need to be eliminated from analysis by creation of an exclusion list. We believe that both CuAAC and RuAAC reactions coupled to LC-MS/MS represent a method for the untargeted identification of acetylenic natural products, but each method has strengths and weaknesses.

Determining the absolute configuration of vanitaracin A, an anti-hepatitis B virus agent

Vanitaracin A is an anti-hepatitis B virus (anti-HBV) compound isolated from the culture broth of the fungus Talaromyces sp. Vanitaracin A inhibits the entry of HBV into target cells with sub-micromolar IC₅₀ values. While a structure-activity relationship study is highly desirable, a synthetic approach still needs to be developed, which is difficult because the absolute configurations of the six stereogenic centers in the structure of vanitaracin A have not yet been determined. In the present study, we used the crystalline sponge method to clarify the configuration of the compound after determining the absolute configuration of the secondary alcohol using a modified Mosher ester method. Combining these analyses with the NOESY spectrum of vanitaracin A and NMR analyses of the crude side-chain carboxylic acid obtained by the alkaline hydrolysis of vanitaracin A revealed the absolute configurations of all stereogenic centers in this important compound.

Solvent Effects in the Crystalline Sponge Method: Importance of Co-solvents for Ordering Absorbed Guests

In the crystalline sponge method, the crucial step for ordering the absorbed guest is soaking of the guest into the pores of the crystalline sponge. Here, we find that the choice of solvent is particularly important for smooth guest soaking and ordering. Moderately polar solvents, such as ketones and esters, which we have previously avoided for the guest-soaking process, efficiently promote diffusion and guest ordering by filling the gaps in the pores through co-crystallization with the guests. Using this modified protocol, we successfully demonstrate the structural analysis of various steroids.

Polyacetylene Glycosides: Isolation, Biological Activities and Synthesis

Polyacetylene glycosides (PAGs) constitute a relatively small class of secondary metabolites characterized by the presence of a sugar unit anomerically connected to a polyacetylene. These compounds are found in fungi, seaweed, and more often in plants. PAGs exhibit a wide range of biological and pharmacological activities and, as a result, the literature of these compounds has grown exponentially in recent years.

A polyyne toxin produced by an antagonistic bacterium blinds and lyses a Chlamydomonad alga

Algae live in association with microbes that interact by a variety of chemical mediators, resulting in mutualistic or antagonistic relationships. Although algae are key contributors to carbon fixation and are fundamental for food webs, we still know little about the underlying molecular mechanisms affecting their fitness. This study investigates the interaction between an antagonistic bacterium and a unicellular alga. It demonstrates multiple roles of a polyyne, protegencin, that is used by the bacteria to attack green algal cells. It is a highly effective toxin that alters a subcellular algal compartment used for vision, bleaches, and lyses the algal cells. These results expand our knowledge of the arsenal of chemical mediators in bacteria and their modes of action in algal communities.

Algae are key contributors to global carbon fixation and form the basis of many food webs. In nature, their growth is often supported or suppressed by microorganisms. The bacterium Pseudomonas protegens Pf-5 arrests the growth of the green unicellular alga Chlamydomonas reinhardtii, deflagellates the alga by the cyclic lipopeptide orfamide A, and alters its morphology [P. Aiyar et al., Nat. Commun. 8, 1756 (2017)]. Using a combination of Raman microspectroscopy, genome mining, and mutational analysis, we discovered a polyyne toxin, protegencin, which is secreted by P. protegens, penetrates the algal cells, and causes destruction of the carotenoids of their primitive visual system, the eyespot. Together with secreted orfamide A, protegencin thus prevents the phototactic behavior of C. reinhardtii. A mutant of P. protegens deficient in protegencin production does not affect growth or eyespot carotenoids of C. reinhardtii. Protegencin acts in a direct and destructive way by lysing and killing the algal cells. The toxic effect of protegencin is also observed in an eyeless mutant and with the colony-forming Chlorophyte alga Gonium pectorale. These data reveal a two-pronged molecular strategy involving a cyclic lipopeptide and a conjugated tetrayne used by bacteria to attack select Chlamydomonad algae. In conjunction with the bloom-forming activity of several chlorophytes and the presence of the protegencin gene cluster in over 50 different Pseudomonas genomes [A. J. Mullins et al., bioRxiv [Preprint] (2021). https://www.biorxiv.org/content/10.1101/2021.03.05.433886v1 (Accessed 17 April 2021)], these data are highly relevant to ecological interactions between Chlorophyte algae and Pseudomonadales bacteria.

Crystalline sponge X-ray analysis coupled with supercritical fluid chromatography: a novel analytical platform for the rapid separation, isolation, and characterization of analytes

Crystalline sponge (CS) based X-ray diffraction (XRD) analysis allows for the observation of the structure of an analyte, including its absolute configuration. Herein we report a powerful analytical platform for the separation, isolation, and structural elucidation of a target analyte in a seamless way by coupling supercritical fluid chromatography (SFC) with CS-based XRD analysis (SFC-CSXRD). The efficacy of this methodology is demonstrated by the rapid characterization of regio- and stereoisomers using three types of CSs with differing tolerances to the solvents used in SFC and guest-soaking.

Discovery of the Pseudomonas Polyyne Protegencin by a Phylogeny-Guided Study of Polyyne Biosynthetic Gene Cluster Diversity

Natural products that possess alkyne or polyyne moieties have been isolated from a variety of biological sources and possess a broad a range of bioactivities. In bacteria, the basic biosynthesis of polyynes is known, but their biosynthetic gene cluster (BGC) distribution and evolutionary relationship to alkyne biosynthesis have not been addressed. Through comprehensive genomic and phylogenetic analyses, the distribution of alkyne biosynthesis gene cassettes throughout bacteria was explored, revealing evidence of multiple horizontal gene transfer events. After investigation of the evolutionary connection between alkyne and polyyne biosynthesis, a monophyletic clade was identified that possessed a conserved seven-gene cassette for polyyne biosynthesis that built upon the conserved three-gene cassette for alkyne biosynthesis. Further diversity mapping of the conserved polyyne gene cassette revealed a phylogenetic subclade for an uncharacterized polyyne BGC present in several Pseudomonas species, designated pgn. Pathway mutagenesis and high-resolution analytical chemistry showed the Pseudomonas protegenspgn BGC directed the biosynthesis of a novel polyyne, protegencin. Exploration of the biosynthetic logic behind polyyne production, through BGC mutagenesis and analytical chemistry, highlighted the essentiality of a triad of desaturase proteins and a thioesterase in both the P. protegenspgn and Trinickia caryophylli (formerly Burkholderia caryophylli) caryoynencin pathways. We have unified and expanded knowledge of polyyne diversity and uniquely demonstrated that alkyne and polyyne biosynthetic gene clusters are evolutionarily related and widely distributed within bacteria. The systematic mapping of conserved biosynthetic genes across the available bacterial genomic diversity proved to be a fruitful method for discovering new natural products and better understanding polyyne biosynthesis.

It Takes Two to Tango: A Bacterial Biofilm Provides Protection against a Fungus-Feeding Bacterial Predator

Fungus-bacterium interactions are widespread, encompass multiple interaction types from mutualism to parasitism, and have been frequent targets for microbial inoculant development. In this study, using in vitro systems combined with confocal laser scanning microscopy and real-time quantitative PCR, we test whether the nitrogen-fixing bacterium Kosakonia radicincitans can provide protection to the plant-beneficial fungus Serendipita indica, which inhabits the rhizosphere and colonizes plants as an endophyte, from the fungus-feeding bacterium Collimonas fungivorans. We show that K. radicincitans can protect fungal hyphae from bacterial feeding on solid agar medium, with probable mechanisms being quick hyphal colonization and biofilm formation. We furthermore find evidence for different feeding modes of K. radicincitans and C. fungivorans, namely “metabolite” and “hyphal feeding”, respectively. Overall, we demonstrate, to our knowledge, the first evidence for a bacterial, biofilm-based protection of fungal hyphae against attack by a fungus-feeding, bacterial predator on solid agar medium. Besides highlighting the importance of tripartite microbial interactions, we discuss implications of our results for the development and application of microbial consortium-based bioprotectants and biostimulants.

Identification of Collimonas gene loci involved in the biosynthesis of a diffusible secondary metabolite with broad-spectrum antifungal activity and plant-protective properties

In greenhouse and field trials, a bacterial mixture of Collimonas arenae Cal35 and Bacillus velezensis FZB42, but not Cal35 alone or FZB42 alone, was able to protect tomato plants from challenge with the soilborne fungal pathogen Fusarium oxysporum f.sp. lycopersici (Fol). To identify genes and mechanisms underlying this property in Cal35, we screened a random transposon insertion library for loss of function and identified two mutants that were impaired completely or partially in their ability to halt the growth of a wide range of fungal species. In mutant 46A06, the transposon insertion was located in a biosynthetic gene cluster that was predicted to code for a hybrid polyketide synthase-non-ribosomal peptide synthetase, while mutant 60C09 was impacted in a gene cluster for the synthesis and secretion of sugar repeat units. Our data are consistent with a model in which both gene clusters are necessary for the production of an antifungal compound we refer to as carenaemins. We also show that the ability to produce carenaemin contributed significantly to the observed synergy between Cal35 and FZB42 in protecting tomato plants from Fol. We discuss the potential for supplementing Bacillus-based biocontrol products with Collimonas bacteria to boost efficacy of such products.

Repeated Exposure of Aspergillus niger Spores to the Antifungal Bacterium Collimonas fungivorans Ter331 Selects for Delayed Spore Germination

The bacterial strain Collimonas fungivorans Ter331 (CfTer331) inhibits mycelial growth and spore germination in Aspergillus niger N402 (AnN402). The mechanisms underlying this antagonistic bacterial-fungal interaction have been extensively studied, but knowledge on the long-term outcome of this interaction is currently lacking. Here, we used experimental evolution to explore the dynamics of fungal adaptation to recurrent exposure to CfTer331. Specifically, five single-spore isolates (SSIs) of AnN402 were evolved under three selection scenarios in liquid culture, i.e., (i) in the presence of CfTer331 for 80 growth cycles, (ii) in the absence of the bacterium for 80 cycles, and (iii) in the presence of CfTer331 for 40 cycles and then in its absence for 40 cycles. The evolved SSI lineages were then evaluated for phenotypic changes from the founder fungal strain, such as germinability with or without CfTer331. The analysis showed that recurrent exposure to CfTer331 selected for fungal lineages with reduced germinability and slower germination, even in the absence of CfTer331. In contrast, when AnN402 evolved in the absence of the bacteria, lineages with increased germinability and faster germination were favored. SSIs that were first evolved in the presence of CfTer331 and then in its absence showed intermediate phenotypes but overall were more similar to SSIs that evolved in the absence of CfTer331 for 80 cycles. This suggests that traits acquired from exposure to CfTer331 were reversible upon removal of the selection pressure. Overall, our study provides insights into the effects on fungi from the long-term coculture with bacteria. IMPORTANCE The use of antagonistic bacteria for managing fungal diseases is becoming increasingly popular, and thus there is a need to understand the implications of their long-term use against fungi. Most efforts have so far focused on characterizing the antifungal properties and mode of action of the bacterial antagonists, but the possible outcomes of the persisting interaction between antagonistic bacteria and fungi are not well understood. In this study, we used experimental evolution in order to explore the evolutionary aspects of an antagonistic bacterial-fungal interaction, using the antifungal bacterium Collimonas fungivorans and the fungus Aspergillus niger as a model system. We show that evolution in the presence or absence of the bacteria selects for fungal lineages with opposing and conditionally beneficial traits, such as slow and fast spore germination, respectively. Overall, our studies reveal that fungal responses to biotic factors related to antagonism could be to some extent predictable and reversible.

Application of Crystalline Matrices for the Structural Determination of Organic Molecules

While single-crystal X-ray diffraction (SC-XRD) is one of the most powerful structural determination techniques for organic molecules, the requirement of obtaining a suitable crystal for analysis limits its applicability, particularly for liquids and amorphous solids. The emergent use of preformed porous crystalline matrices that can absorb organic compounds and stabilize them via host-guest interactions for observation via SC-XRD offers a way to overcome this hindrance. A topical and current discussion of SC-XRD in organic chemistry and the use of preformed matrices for the in crystallo analysis of organic compounds, with a particular focus on the absolute structure determination of chiral molecules, is presented. Preformed crystalline matrices that are covered include metal-organic frameworks (MOFs) as used in the crystalline sponge method, metal-organic polyhedra (MOPs, coordination cages), porous organic materials (POMs)/porous organic molecular crystals (POMCs), and biological scaffolds. An outlook and perspective on the current technology and on its future directions is provided.

Chemical signals driving bacterial-fungal interactions

Microorganisms reside in diverse environmental communities where interactions become indispensable due to close physical associations. These interactions are driven by chemical communication among different microbial kingdoms, particularly between fungi and bacteria. Knowledge about these communication signals provides useful information about the nature of microbial interactions and allows predictions of community development in diverse environments. Here, we provide an update on the role of small signalling molecules in fungal-bacterial interactions with focus on agricultural and medicinal environments. This review highlights the range of - and response to - diverse biochemicals produced by both kingdoms with view to harnessing their properties towards drug discovery applications.

Streptomyces sp. strain TOR3209: a rhizosphere bacterium promoting growth of tomato by affecting the rhizosphere microbial community

Aiming at revealing the possible mechanism of its growth promoting effect on tomato, the correlations among Streptomyces sp. TOR3209 inoculation, rhizobacteriome, and tomato growth/production traits were investigated in this study. By analyses of Illumina sequencing and plate coating, differences in rhizosphere microbial communities were found in different growth stages and distinct inoculation treatments. The plant biomass/fruit yields and relative abundances of families Flavobacteriaceae, Sphingobacteriaceae, Polyangiaceae and Enterobacteriaceae in treatments T (tomato inoculated with TOR3209) and TF (tomato inoculated with TOR3209 + organic fertilizer) were higher than that in the controls (CK and CK+ organic fertilizer), respectively. The analysis of Metastats and LEfSe revealed that the genera Flavobacterium and Sorangium in seedling stage, Klebsiella in flowering stage, Collimonas in early fruit setting stage, and genera Micrococcaceae, Pontibacte and Adhaeribacter in late fruit setting stage were the most representative rhizobacteria that positively responded to TOR3209 inoculation. By cultivation method, five bacterial strains positively correlated to TOR3209 inoculation were isolated from rhizosphere and root endosphere, which were identified as tomato growth promoters affiliated to Enterobacter sp., Arthrobacter sp., Bacillus subtilis, Rhizobium sp. and Bacillus velezensis. In pot experiment, TOR3209 and B. velezensis WSW007 showed joint promotion to tomato production, while the abundance of inoculated TOR3209 was dramatically decreased in rhizosphere along the growth of tomato. Conclusively, TOR3209 might promote the tomato production via changing of microbial community in rhizosphere. These findings provide a better understanding of the interactions among PGPR in plant promotion.

An Expansion of Crystalline Sponge X-ray Analysis to Elucidate the Molecular Structure of Reactive Compounds via Ion Pair Formation

The crystalline sponge (CS) method allows structural elucidation of a target compound (guest) in solution by single crystal X-ray diffraction through trapping the guest into the CS framework. In principle, the CS method is inapplicable to reactive compounds that break the CS framework, such as acidic, basic, or nucleophilic ones. Here, a solution to this problem is disclosed wherein an ion pair of the guest compound is formed during the guest-soaking step by adding a suitable reagent. The ion pair can be observed and does not damage the CS framework. Using the developed method, amino, guanidino, and amidino compounds have been successfully analyzed as ion pairs with sulfonic acids. Practical utility has been shown because the absolute configurations of optically resolved amine derivatives were revealed with only a few micrograms. This demonstrates that the ion-pair-soaking method is simple and expands the range of compounds applicable to the CS method.

Identification of Feldin, an Antifungal Polyyne from the Beefsteak Fungus Fistulina hepatica

Fruiting body-forming members of the Basidiomycota maintain their ecological fitness against various antagonists like ascomycetous mycoparasites. To achieve that, they produce myriads of bioactive compounds, some of which are now being used as agrochemicals or pharmaceutical lead structures. Here, we screened ethyl acetate crude extracts from cultures of thirty-five mushroom species for antifungal bioactivity, for their effect on the ascomycete Saccharomyces cerevisiae and the basidiomycete Ustilago maydis. One extract that inhibited the growth of S. cerevisiae much stronger than that of U. maydis was further analyzed. For bioactive compound identification, we performed bioactivity-guided HPLC/MS fractionation. Fractions showing inhibition against S. cerevisiae but reduced activity against U. maydis were further analyzed. NMR-based structure elucidation from one such fraction revealed the polyyne we named feldin, which displays prominent antifungal bioactivity. Future studies with additional mushroom-derived eukaryotic toxic compounds or antifungals will show whether U. maydis could be used as a suitable host to shortcut an otherwise laborious production of such mushroom compounds, as could recently be shown for heterologous sesquiterpene production in U. maydis.

Chemical Mediators at the Bacterial-Fungal Interface

Interactions among microbes are key drivers of evolutionary progress and constantly shape ecological niches. Microorganisms rely on chemical communication to interact with each other and surrounding organisms. They synthesize natural products as signaling molecules, antibiotics, or modulators of cellular processes that may be applied in agriculture and medicine. Whereas major insight has been gained into the principles of intraspecies interaction, much less is known about the molecular basis of interspecies interplay. In this review, we summarize recent progress in the understanding of chemically mediated bacterial-fungal interrelations. We discuss pairwise interactions among defined species and systems involving additional organisms as well as complex interactions among microbial communities encountered in the soil or defined as microbiota of higher organisms. Finally, we give examples of how the growing understanding of microbial interactions has contributed to drug discovery and hypothesize what may be future directions in studying and engineering microbiota for agricultural or medicinal purposes.

Crystalline Sponges as a Sensitive and Fast Method for Metabolite Identification: Application to Gemfibrozil and its Phase I and II Metabolites

Understanding the metabolism of new drug candidates is important during drug discovery and development, as circulating metabolites may contribute to efficacy or cause safety issues. In the early phase of drug discovery, human in vitro systems are used to investigate human relevant metabolism. Though conventional techniques are limited in their ability to provide complete molecular structures of metabolites (liquid chromatography mass spectrometry) or require a larger amount of material not available from in vitro incubation (nuclear magnetic resonance), we here report for the first time the use of the crystalline sponge method to identify phase I and phase II metabolites generated from in vitro liver microsomes or S9 fractions. Gemfibrozil was used as a test compound. Metabolites generated from incubation with microsomes or S9 fractions, were fractionated using online fraction collection. After chromatographic purification and fractionation of the generated metabolites, single crystal X-ray diffraction of crystalline sponges was used to identify the structure of gemfibrozil metabolites. This technique allowed for complete structure elucidation of 5'-CH2OH gemfibrozil (M1), 4'-OH gemfibrozil (M2), 5'-COOH gemfibrozil (M3), and the acyl glucuronide of gemfibrozil, 1-O-β-glucuronide (M4), the first acyl glucuronide available in the Cambridge Crystallographic Data Centre. Our study shows that when optimal soaking is possible, crystalline sponges technology is a sensitive (nanogram amount) and fast (few days) method that can be applied early in drug discovery to identify the structure of pure metabolites from in vitro incubations. SIGNIFICANCE STATEMENT: Complete structure elucidation of human metabolites plays a critical role in early drug discovery. Low amounts of material (nanogram) are only available at this stage and insufficient for nuclear magnetic resonance analysis. The crystalline sponge method has the potential to close this gap, as demonstrated in this study.

Interruption of Aspergillus niger spore germination by the bacterially produced secondary metabolite collimomycin

Collimonas fungivorans Ter331 (CfTer331) is a soil bacterium that produces collimomycin, a secondary metabolite that inhibits the vegetative growth of fungi. Here we show that CfTer331 can also interfere with fungal spore germination and that collimomycin biosynthesis is required for this activity. More specifically, in co-cultures of Aspergillus niger N402 (AnN402) co-nidiospores with CfTer331, the rate of transition from the isotropic to polarized stage of the germination process was reduced and the relatively few AnN402 conidiospores that completed the germination process were less likely to survive than those that were arrested in the isotropic phase. By contrast, a collimomycin-deficient mutant of CfTer331 had no effect on germination: in its presence, as in the absence or delayed presence of CfTer331, unhindered germination of conidiospores allowed rapid establishment of AnN402 mycelium and the subsequent acidification of the culture medium to the detriment of any bacteria present. However, when challenged early enough with CfTer331, the collimomycin-dependent arrest of the AnN402 germination process enabled CfTer331 to prevent AnN402 from forming mycelia and to gain dominance in the culture. We propose that the collimomycin-dependent arrest of spore germination represents an early intervention strategy used by CfTer331 to mitigate niche construction by fungi in nature.

Survey of natural products reported by Asian research groups in 2018

The new natural products reported in 2018 in peer-reviewed articles in journals with good reputations were reviewed and analyzed. The advances made by Asian research groups in the field of natural products chemistry in 2018 were summarized. Compounds with unique structural features and/or promising bioactivities originating from Asian natural sources were discussed based on their structural classification.

Natural Products as a Foundation for Drug Discovery

Many natural products have been used as drugs for the treatment of diverse indications. Although most U.S. pharmaceutical companies have reduced or eliminated their in-house natural-product research over the years, new approaches for compound screening and chemical synthesis are resurrecting interest in exploring the therapeutic value of natural products. The aim of this commentary is to review emerging strategies and techniques that have made natural products a viable strategic choice for inclusion in drug discovery programs. Published 2019. U.S. Government.

Bioorganic chemistry of signaling molecules in microbial communication

Microorganisms produce and secrete a variety of secondary metabolites including fatty acids, polyketides, terpenoids, alkaloids, and peptides. Among them, many molecules act as chemical signals that play important roles in inter-/intra-species microbial communication or the interaction with host organisms. In this review, I focus on our recent reports of the microbial signaling molecules involved in bacterium-fungus, bacterium-plant, and fungus-plant interactions. Their potential contribution to pest management is also discussed.

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

A putative siderophore locus was detected in the genome of the violacein-producing bacterium Massilia sp. NR 4-1 and predicted to direct the biosynthesis of a molecule that is structurally related to the thiazoline-containing siderophore micacocidin. In order to track this compound, we analyzed the metabolic profiles of Massilia cultures grown under different iron concentrations. A compound which was found to be predominantly produced under iron deficiency was subsequently isolated. Its structural characterization by spectroscopic and bioinformatic analyses revealed a previously not known diastereomer of the cytotoxic alkaloid agrochelin. The structure of this natural product, which was named massiliachelin, corresponds to the assembly line encoded by the identified siderophore locus.

Genome mining identifies cepacin as a plant-protective metabolite of the biopesticidal bacterium Burkholderia ambifaria

Beneficial microorganisms are widely used in agriculture for control of plant pathogens, but a lack of efficacy and safety information has limited the exploitation of multiple promising biopesticides. We applied phylogeny-led genome mining, metabolite analyses and biological control assays to define the efficacy of Burkholderia ambifaria, a naturally beneficial bacterium with proven biocontrol properties but potential pathogenic risk. A panel of 64 B. ambifaria strains demonstrated significant antimicrobial activity against priority plant pathogens. Genome sequencing, specialized metabolite biosynthetic gene cluster mining and metabolite analysis revealed an armoury of known and unknown pathways within B. ambifaria. The biosynthetic gene cluster responsible for the production of the metabolite cepacin was identified and directly shown to mediate protection of germinating crops against Pythium damping-off disease. B. ambifaria maintained biopesticidal protection and overall fitness in the soil after deletion of its third replicon, a non-essential plasmid associated with virulence in Burkholderia cepacia complex bacteria. Removal of the third replicon reduced B. ambifaria persistence in a murine respiratory infection model. Here, we show that by using interdisciplinary phylogenomic, metabolomic and functional approaches, the mode of action of natural biological control agents related to pathogens can be systematically established to facilitate their future exploitation.

Synthesis of 1,3-Diynes via Cadiot-Chodkiewicz Coupling of Volatile, in Situ Generated Bromoalkynes

A convenient Cadiot-Chodkiewicz protocol that facilitates the use of low molecular weight alkyne coupling partners is described. The method entails an in situ elimination from a dibromoolefin precursor and immediate subjection to copper-catalyzed conditions, circumventing the hazards of volatile brominated alkynes. The scope of this method is described, and the internal 1,3-diyne products are preliminarily evaluated in ruthenium-catalyzed azide-alkyne cycloadditions.