Discovery and Biosynthesis of Gladiolin: A Burkholderia gladioli Antibiotic with Promising Activity against Mycobacterium tuberculosis

The Myxobacterial Genus Archangium: A Prolific and Underexploited Source of Bioactive Secondary Metabolites

The genus Archangium, a cryptic group of myxobacteria, is a rich source of diverse secondary metabolites. This study reviews the chemical structures and discovery history of 55 secondary metabolites, analyzing the relationship between the chemical structures of these compounds and their bioactivity profiles through molecular networking. Notably, 63.6% of the compounds exhibit potent antimicrobial (MIC < 1 μg/mL) and/or cytotoxic activities (IC50 < 1 μg/mL). Advances in the biosynthetic gene clusters and biosynthetic pathways of seven classes of identified compounds are also presented. Finally, genomic mining approaches are applied to analyze the potential for Archangium strains to synthesize analogs of identified bioactive natural products, uncovering that 98.7% of their secondary metabolic potential remains unexplored. This study highlights the vast potential of Archangium bacteria in synthesizing clade-specific novel secondary metabolites, particularly ribosomally synthesized and post-translationally modified peptide natural products, offering valuable insights for the targeted discovery and biosynthesis of new natural products from this genus.

Molecular Basis for Short-Chain Thioester Hydrolysis by Acyl Hydrolases in trans-Acyltransferase Polyketide Synthases

Polyketide synthases (PKSs) are multidomain enzymatic assembly lines that biosynthesize a wide selection of bioactive natural products from simple building blocks. In contrast to their cis-acyltransferase (AT) counterparts, trans-AT PKSs rely on stand-alone ATs to load extender units onto acyl carrier protein (ACP) domains embedded in the core PKS machinery. Trans-AT PKS gene clusters also encode stand-alone acyl hydrolases (AHs), which are predicted to share the overall fold of ATs but function like type II thioesterases (TEIIs), hydrolyzing aberrant acyl chains from ACP domains to promote biosynthetic efficiency. How AHs specifically target short acyl chains, in particular acetyl groups, tethered as thioesters to the substrate-shuttling ACP domains, with hydrolytic rather than acyl transfer activity, has remained unclear. To answer these questions, we solved the first structure of an AH and performed structure-guided activity assays on active site variants. Our results offer key insights into chain length control and selection against coenzyme A-tethered substrates, and clarify how the interaction interface between AHs and ACP domains contributes to recognition of cognate and noncognate ACP domains. Combining our experimental findings with molecular dynamics simulations allowed for the construction of a data-driven model of an AH:ACP domain complex. Our results advance the currently incomplete understanding of polyketide biosynthesis by trans-AT PKSs, and provide foundations for future bioengineering efforts to offload biosynthetic intermediates or enhance product yields.

Discovery of Cryptic Natural Products Using High-Throughput Elicitor Screening on Agar Media

It is now well-established that microbial genomes carry sparingly expressed biosynthetic gene clusters (BGCs) that need to be induced in order to characterize their products. To do so, we herein subjected two well-known producers, Burkholderia plantarii and Burkholderia gladioli, to high-throughput elicitor screening (HiTES), an emerging approach for accessing the products of these "cryptic" BGCs. Both organisms have previously been examined extensively in liquid cultures. We therefore applied HiTES on agar and found several novel natural products that are only produced in this format and not in liquid cultures. Most notably we found two metabolites, termed burkethyl A and B, that contain an unusual m-ethylbenzoyl group and for which we identified the cognate BGC using bioinformatic and genetic studies. Our results indicate that agar-based HiTES is a promising approach for natural product discovery and are in line with the notion that even "drained" strains remain sources of new metabolites as long as alternative approaches are employed.

Gladiolin produced by pathogenic Burkholderia synergizes with amphotericin B through membrane lipid rearrangements

Amphotericin B (AmpB) is an effective but toxic antifungal drug. Thus, improving its activity/toxicity relationship is of interest. AmpB disrupts fungal membranes by two proposed mechanisms: ergosterol sequestration from the membrane and pore formation. Whether these two mechanisms operate in conjunction and how they could be potentiated remains to be fully understood. Here, we report that gladiolin, a polyketide antibiotic produced by Burkholderia gladioli, is a strong potentiator of AmpB and acts synergistically against Cryptococcus and Candida species, including drug-resistant C. auris. Gladiolin also synergizes with AmpB against drug-resistant fungal biofilms, while exerting no mammalian cytotoxicity. To explain the mechanism of synergy, we show that gladiolin interacts with membranes via a previously unreported binding mode for polyketides. Moreover, gladiolin modulates lipid binding by AmpB and, in combination, causes faster and more pronounced lipid rearrangements relative to AmpB alone which include membrane thinning consistent with ergosterol extraction, areas of thickening, pore formation, and increased membrane destruction. These biophysical data provide evidence of a functional interaction between gladiolin and AmpB at the membrane interface. The data further indicate that the two proposed AmpB mechanisms (ergosterol sequestration and pore formation) act in conjunction to disrupt membranes, and that gladiolin synergizes by enhancing both mechanisms. Collectively, our findings shed light on AmpB's mechanism of action and characterize gladiolin as an AmpB potentiator, showing an antifungal mechanism distinct from its proposed antibiotic activity. We shed light on the synergistic mechanism at the membrane, and provide insights into potentiation strategies to improve AmpB's activity/toxicity relationship.

IMPORTANCE

Amphotericin B (AmpB) is one of the oldest antifungal drugs in clinical use. It is an effective therapeutic, but it comes with toxicity issues due to the similarities between its fungal target (the membrane lipid ergosterol) and its mammalian counterpart (cholesterol). One strategy to improve its activity/toxicity relationship is by combinatorial therapy with potentiators, which would enable a lower therapeutic dose of AmpB. Here, we report on the discovery of the antibiotic gladiolin as a potentiator of AmpB against several priority human fungal pathogens and fungal biofilms, with no increased toxicity against mammalian cells. We show that gladiolin potentiates AmpB by increasing and accelerating membrane damage. Our findings also provide insights into the on-going debate about the mechanism of action of AmpB by indicating that both proposed mechanisms, extraction of ergosterol from membranes and pore formation, are potentiated by gladiolin.

Recent Advances in Discovery, Structure, Bioactivity, and Biosynthesis of trans-AT Polyketides

Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are among the most complex enzymes, which are responsible for generating a wide range of natural products, identified as trans-AT polyketides. These polyketides have received significant attention in drug development due to their structural diversity and potent bioactivities. With approximately 300 synthesized molecules discovered so far, trans-AT PKSs are found widespread in bacteria. Their biosynthesis pathways exhibit considerable genetic diversity, leading to the emergence of numerous enzymes with novel mechanisms, serving as a valuable resource for genetic engineering aimed at modifying small molecules' structures and creating new engineered enzymes. Despite the systematic discussions on trans-AT polyketides and their biosynthesis in earlier studies, the continuous advancements in tools, methods, compound identification, and biosynthetic pathways require a fresh update on accumulated knowledge. This review seeks to provide a comprehensive discussion for the 27 types of trans-AT polyketides discovered within the last seven years, detailing their sources, structures, biological activities, and biosynthetic pathways. By reviewing this new knowledge, a more profound understanding of the trans-AT polyketide family can be achieved.

Invasibility of a North American soil ecosystem to amphibian-killing fungal pathogens

North American salamanders are threatened by intercontinental spread of chytridiomycosis, a deadly disease caused by the fungal pathogen Batrachochytrium salamandrivorans (Bsal). To predict potential dispersal of Bsal spores to salamander habitats, we evaluated the capacity of soil microbial communities to resist invasion. We determined the degree of habitat invasibility using soils from five locations throughout the Great Smoky Mountains National Park, a region with a high abundance of susceptible hosts. Our experimental design consisted of replicate soil microcosms exposed to different propagule pressures of the non-native pathogen, Bsal, and an introduced but endemic pathogen, B. dendrobatidis (Bd). To compare growth and competitive interactions, we used quantitative PCR, live/dead cell viability assays, and full-length 16S rRNA sequencing. We found that soil microcosms with intact bacterial communities inhibited both Bsal and Bd growth, but inhibitory capacity diminished with increased propagule pressure. Bsal showed greater persistence than Bd. Linear discriminant analysis (LDA) identified the family Burkolderiaceae as increasing in relative abundance with the decline of both pathogens. Although our findings provide evidence of environmental filtering in soils, such barriers weakened in response to pathogen type and propagule pressure, showing that habitats vary their invasibility based on properties of their local microbial communities.

Antibiotic Skeletal Diversification via Differential Enoylreductase Recruitment and Module Iteration in trans-Acyltransferase Polyketide Synthases

Microorganisms are remarkable chemists capable of assembling complex molecular architectures that penetrate cells and bind biomolecular targets with exquisite selectivity. Consequently, microbial natural products have wide-ranging applications in medicine and agriculture. How the "blind watchmaker" of evolution creates skeletal diversity is a key question in natural products research. Comparative analysis of biosynthetic pathways to structurally related metabolites is an insightful approach to addressing this. Here, we report comparative biosynthetic investigations of gladiolin, a polyketide antibiotic from Burkholderia gladioli with promising activity against multidrug-resistant Mycobacterium tuberculosis, and etnangien, a structurally related antibiotic produced by Sorangium cellulosum. Although these metabolites have very similar macrolide cores, their C21 side chains differ significantly in both length and degree of saturation. Surprisingly, the trans-acyltransferase polyketide synthases (PKSs) that assemble these antibiotics are almost identical, raising intriguing questions about mechanisms underlying structural diversification in this important class of biosynthetic assembly line. In vitro reconstitution of key biosynthetic transformations using simplified substrate analogues, combined with gene deletion and complementation experiments, enabled us to elucidate the origin of all the structural differences in the C21 side chains of gladiolin and etnangien. The more saturated gladiolin side chain arises from a cis-acting enoylreductase (ER) domain in module 1 and in trans recruitment of a standalone ER to module 5 of the PKS. Remarkably, module 5 of the gladiolin PKS is intrinsically iterative in the absence of the standalone ER, accounting for the longer side chain in etnangien. These findings have important implications for biosynthetic engineering approaches to the creation of novel polyketide skeletons.

Insights into group-specific pattern of secondary metabolite gene cluster in Burkholderia genus

Burkholderia is a versatile strain that has expanded into several genera. It has been steadily reported that the genome features of Burkholderia exhibit activities ranging from plant growth promotion to pathogenicity across various isolation areas. The objective of this study was to investigate the secondary metabolite patterns of 366 Burkholderia species through comparative genomics. Samples were selected based on assembly quality assessment and similarity below 80% in average nucleotide identity. Duplicate samples were excluded. Samples were divided into two groups using FastANI analysis. Group A included B. pseudomallei complex. Group B included B. cepacia complex. The limitations of MLST were proposed. The detection of genes was performed, including environmental and virulence-related genes. In the pan-genome analysis, each complex possessed a similar pattern of cluster for orthologous groups. Group A (n = 185) had 14,066 cloud genes, 2,465 shell genes, 682 soft-core genes, and 2,553 strict-core genes. Group B (n = 181) had 39,867 cloud genes, 4,986 shell genes, 324 soft-core genes, 222 core genes, and 2,949 strict-core genes. AntiSMASH was employed to analyze the biosynthetic gene cluster (BGC). The results were then utilized for network analysis using BiG-SCAPE and CORASON. Principal component analysis was conducted and a table was constructed using the results obtained from antiSMASH. The results were divided into Group A and Group B. We expected the various species to show similar patterns of secondary metabolite gene clusters. For in-depth analysis, a network analysis of secondary metabolite gene clusters was conducted, exemplified by BiG-SCAPE analysis. Depending on the species and complex, Burkholderia possessed several kinds of siderophore. Among them, ornibactin was possessed in most Burkholderia and was clustered into 4,062 clans. There was a similar pattern of gene clusters depending on the species. NRPS_04014 belonged to siderophore BGCs including ornibactin and indigoidine. However, it was observed that each family included a similar species. This suggests that, besides siderophores being species-specific, the ornibactin gene cluster itself might also be species-specific. The results suggest that siderophores are associated with environmental adaptation, possessing a similar pattern of siderophore gene clusters among species, which could provide another perspective on species-specific environmental adaptation mechanisms.

Biosynthesis of trans-AT PKS-Derived Shuangdaolides Featuring a trans-acting Enzyme for Online Epoxidation

Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) synthesize natural products with intricate structures and potent biological activities. They generally contain various unusual modules or trans-acting enzymes. Herein, we report the trans-AT PKS-derived biosynthetic pathway of the shuangdaolide with a rare internal 2-hydroxycyclopentenone moiety. The multidomain protein SdlR catalyzes the synthesis of 16,17-epoxide during polyketide chain elongation. The SdlR contains a ketoreductase, an acyl carrier protein, a flavoprotein monooxygenase, and a serine hydrolase domain. This online epoxidation occurs at unusual positions away from the thioester. Then, two tailoring enzymes, SdlB and SdlQ, convert a methylene to a carbonyl group and oxidize a hydroxyl group to a carbonyl group, respectively. The following spontaneous opening of 16,17-epoxide induces the formation of a new C-C bond to generate the 2-hydroxycyclopentenone moiety. The characterization of the shuangdaolide pathway extends the understanding of the trans-AT PKSs, facilitating the mining and identification of this class of natural products.

The Antibacterial and Antibiofilm Activities of the Endophytic Bacteria Associated with Archidendron pauciflorum against Multidrug-Resistant Strains

Endophytes associated with medicinal plants are a potential source of valuable natural products. This study aimed to evaluate the antibacterial and antibiofilm activities of endophytic bacteria from Archidendron pauciflorum against multidrug-resistant (MDR) strains. A total of 24 endophytic bacteria were isolated from the leaf, root, and stem of A. pauciflorum. Seven isolates showed antibacterial activity with different spectra against four MDR strains. Extracts derived from four selected isolates (1 mg/mL) also displayed antibacterial activity. Among four selected isolates, DJ4 and DJ9 isolates exhibited the strongest antibacterial activity against P. aeruginosa strain M18, as indicated by the lowest minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) (DJ4 and DJ9 MIC: 7.81 µg/mL; DJ4 and DJ9 MBC: 31.25 µg/mL). 2 × MIC of DJ4 and DJ9 extracts was found to be the most effective concentration to inhibit more than 52% of biofilm formation and eradicate more than 42% of established biofilm against all MDR strains. 16S rRNA-based identification revealed four selected isolates belong to the genus Bacillus. DJ9 isolate possessed nonribosomal peptide synthetase (NRPS) gene, and DJ4 isolate possessed NRPS and polyketide synthase type I (PKS I) gene. Both these genes are commonly responsible for secondary metabolites synthesis. Several antimicrobial compounds, including 1,4-dihydroxy-2-methyl-anthraquinone and paenilamicin A1, were detected in the bacterial extracts. This study highlights endophytic bacteria isolated from A. pauciflorum provide a great source of novel antibacterial compounds.

Heterologous Biosynthesis of Complex Bacterial Natural Products in Burkholderia gladioli

Bacterial natural products (NPs) are an indispensable source of drugs and biopesticides. Heterologous expression is an essential method for discovering bacterial NPs and the efficient biosynthesis of valuable NPs, but the chassis for Gram-negative bacterial NPs remains inadequate. In this study, we built a Burkholderiales mutant Burkholderia gladioli Δgbn::attB by introducing an integrated site (attB) to inactivate the native gladiolin (gbn) biosynthetic gene cluster, which stabilizes large foreign gene clusters and reduces the native metabolite profile. The growth and successful heterologous production of high-value NPs such as phylogenetically close Burkholderiales-derived antitumor polyketides (PKs) rhizoxins, phylogenetically distant Gammaproteobacteria-derived anti-MRSA (methicillin-resistant Staphylococcus aureus) antibiotics WAP-8294As, and Deltaproteobacteria-derived antitumor PKs disorazols demonstrate that this strain is a potential chassis for Gram-negative bacterial NPs. We further improved the yields of WAP-8294As through promoter insertions and precursor pathway overexpression based on heterologous expression in this strain. This study provides a robust bacterial chassis for genome mining, efficient production, and molecular engineering of bacterial NPs.

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.

Molecular basis for short-chain thioester hydrolysis by acyl hydrolase domains in trans -acyltransferase polyketide synthases

Polyketide synthases (PKSs) are multi-domain enzymatic assembly lines that biosynthesise a wide selection of bioactive natural products from simple building blocks. In contrast to their cis -acyltransferase (AT) counterparts, trans -AT PKSs rely on stand-alone AT domains to load extender units onto acyl carrier protein (ACP) domains embedded in the core PKS machinery. Trans -AT PKS gene clusters also encode acyl hydrolase (AH) domains, which are predicted to share the overall fold of AT domains, but hydrolyse aberrant acyl chains from ACP domains, thus ensuring efficient polyketide biosynthesis. How such domains specifically target short acyl chains, in particular acetyl groups, tethered as thioesters to the substrate-shuttling ACP domains, with hydrolytic rather than acyl transfer activity, has remained unclear. To answer these questions, we solved the first structure of an AH domain and performed structure-guided activity assays on active site variants. Our results offer key insights into chain length control and selection against coenzyme A-tethered substrates, and clarify how the interaction interface between AH and ACP domains contributes to recognition of cognate and non-cognate ACP domains. Combining our experimental findings with molecular dynamics simulations allowed for the production of a data-driven model of an AH:ACP domain complex. Our results advance the currently incomplete understanding of polyketide biosynthesis by trans -AT PKSs, and provide foundations for future bioengineering efforts.

Characterization of three succinyl-CoA acyltransferases involved in polyketide chain assembly

Polyketides are a class of natural products with astonishing structural diversities, fascinating biological activities, and a versatile of applications. In polyketides biosynthesis, acyltransferases (ATs) are the 'gatekeeping' enzymes selecting the specific CoA-activated acyl groups as building blocks and transferring them onto the phosphopantetheine arm of acyl carrier proteins (ACPs) to enable the following condensation reactions to assemble the polyketide chain. Herein, the Art2 protein from aurantinins, a group of the antibacterial polyketides, is characterized in vitro as an AT that can load a CoA-activated succinyl unit onto the first ACP domain of Art17 (ACP_Art17-1). In addition, another two proteins, GbnB and EtnB, involved in the biosynthesis of gladiolin and etnangien respectively, were traced by literature mining, homologous searching, and product structure analysis and then identified as functional succinyl-CoA ATs by the ACP_Art17-1 assays. Taken together, by the assay method employing ACP_Art17-1 as an acyl acceptor, we identified three ATs that can introduce a succinyl unit into the polyketide assembly line, which enriches the toolbox of polyketide biosynthetic enzymes and sets a stage for incorporating a succinyl unit into polyketide backbones in synthetic biological manners. KEY POINTS: • Three acyltransferases that are able to load ACP with a succinyl unit were characterized in vitro. • ACP_Art17-1 can be used as an acceptor to assay succinyl-CoA AT from different polyketides. • The succinyl unit can be incorporated into polyketides assembly process.

Compilation of the Antimicrobial Compounds Produced by Burkholderia Sensu Stricto

Due to the increase in multidrug-resistant microorganisms, the investigation of novel or more efficient antimicrobial compounds is essential. The World Health Organization issued a list of priority multidrug-resistant bacteria whose eradication will require new antibiotics. Among them, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae are in the "critical" (most urgent) category. As a result, major investigations are ongoing worldwide to discover new antimicrobial compounds. Burkholderia, specifically Burkholderia sensu stricto, is recognized as an antimicrobial-producing group of species. Highly dissimilar compounds are among the molecules produced by this genus, such as those that are unique to a particular strain (like compound CF66I produced by Burkholderia cepacia CF-66) or antimicrobials found in a number of species, e.g., phenazines or ornibactins. The compounds produced by Burkholderia include N-containing heterocycles, volatile organic compounds, polyenes, polyynes, siderophores, macrolides, bacteriocins, quinolones, and other not classified antimicrobials. Some of them might be candidates not only for antimicrobials for both bacteria and fungi, but also as anticancer or antitumor agents. Therefore, in this review, the wide range of antimicrobial compounds produced by Burkholderia is explored, focusing especially on those compounds that were tested in vitro for antimicrobial activity. In addition, information was gathered regarding novel compounds discovered by genome-guided approaches.

Selection of Relevant Bacterial Strains for Novel Therapeutic Testing: a Guidance Document for Priority Cystic Fibrosis Lung Pathogens

Purpose of Review

People with cystic fibrosis (CF) suffer chronic lung infections with a range of antimicrobial-resistant bacterial pathogens. There is an urgent need for researchers to develop novel anti-infectives to treat these problematic infections, but how can we select bacterial strains which are relevant for robust testing and comparative research?

Recent Findings

Pseudomonas aeruginosa, Burkholderia cepacia complex and Burkholderia gladioli, Mycobacterium abscessus complex, Staphylococcus aureus, Haemophilus influenza, and several multidrug-resistant Gram-negative species were selected as key CF infections that urgently require new therapeutics. Reference isolates and strain panels were identified, and a summary of the known genotypic diversity of each pathogen was provided.

Summary

Here, we summarise the current strain resources available for priority CF bacterial pathogens and highlight systematic selection criteria that researchers can use to select strains for use in therapeutic testing.

Dynamic changes in the endophytic bacterial community during maturation of Amorphophallus muelleri seeds

The seed microbiota is considered to be the starting point of the accumulation of plant microbiota, which is conducive to the preservation and germination of seeds and the establishment and development of seedlings. Our understanding of the colonization and migration dynamics of microbial taxa during seed development and maturation is still limited. This study used 16S rRNA high-throughput sequencing to investigate the dynamic changes in the composition and diversity of the endophytic bacterial community during maturation of Amorphophallus muelleri seeds. The results showed that as seeds matured (green to red), the Shannon index of their endophytic bacterial community first decreased and then increased, and the ACE and Chao1 indices of the endophytic bacterial community decreased gradually. The Shannon, ACE, and Chao1 indices of the endophytic bacterial community in the seed coat first decreased and then increased. Principal coordinate analysis of the bacterial communities revealed that the seed coat at different maturity stages showed significantly distinct bacterial communities and formed different clusters according to maturity stage. The bacterial communities of green and red seeds showed a clear separation, but they both overlapped with those of yellow seeds, indicating that some core taxa were present throughout seed maturation, but their relative abundance was dynamically changing. As the seeds grew more mature, the relative abundance of some bacterial communities with plant growth-promoting traits and others correlated with plant resistance (e.g., Burkholderia-Caballeronia-Paraburkholderia, Bacillus, Pseudomonas, Bradyrhizobium, Streptomyces) tended to increase and peaked in fully mature seeds and seed coats. The endophytic bacterial community of A. muelleri seeds seems to be driven by the seed maturation state, which can provide a theoretical basis for a comprehensive understanding of the assembly process of the microbial community during A. muelleri seed maturation.

Beyond the approved: target sites and inhibitors of bacterial RNA polymerase from bacteria and fungi

Covering: 2016 to 2022RNA polymerase (RNAP) is the central enzyme in bacterial gene expression representing an attractive and validated target for antibiotics. Two well-known and clinically approved classes of natural product RNAP inhibitors are the rifamycins and the fidaxomycins. Rifampicin (Rif), a semi-synthetic derivative of rifamycin, plays a crucial role as a first line antibiotic in the treatment of tuberculosis and a broad range of bacterial infections. However, more and more pathogens such as Mycobacterium tuberculosis develop resistance, not only against Rif and other RNAP inhibitors. To overcome this problem, novel RNAP inhibitors exhibiting different target sites are urgently needed. This review includes recent developments published between 2016 and today. Particular focus is placed on novel findings concerning already known bacterial RNAP inhibitors, the characterization and development of new compounds isolated from bacteria and fungi, and providing brief insights into promising new synthetic compounds.

Guidelines for metabolomics-guided transposon mutagenesis for microbial natural product discovery

There is a great discrepancy between the natural product output of cultured microorganisms and their bioinformatically predicted biosynthetic potential, such that most of the molecular diversity contained within microbial reservoirs has yet to be discovered. One of the primary reasons is insufficient expression of natural product biosynthetic gene clusters (BGCs) under standard laboratory conditions. Several methods have been developed to increase production from such "cryptic" BGCs. Among these, we recently implemented mass spectrometry-guided transposon mutagenesis, a forward genetic screen in which mutants that exhibit stimulated biosynthesis of cryptic metabolites, as read out by mass spectrometry, are selected from a transposon mutant library. Herein, we use Burkholderia gladioli as an example and provide guidelines for generating transposon mutant libraries, measuring metabolomic inventories through mass spectrometry, performing comparative metabolomics to prioritize cryptic natural products from the mutant library, and isolating and characterizing novel natural products elicited through mutagenesis. Application of this approach will be useful in both accessing novel natural products from cryptic BGCs and identifying genes involved in their global regulation.

In silico genome mining of potential novel biosynthetic gene clusters for drug discovery from Burkholderia bacteria

As an emerging resource, Gram-negative Burkholderia bacteria were able to produce a wide range of bioactive secondary metabolites with potential therapeutic and biotechnological applications. Genome mining has emerged as an influential platform for screening and pinpointing natural product diversity with the increasing number of Burkholderia genome sequences. Here, for genome mining of potential biosynthetic gene clusters (BGCs) and prioritizing prolific producing Burkholderia strains, we investigated the relationship between species evolution and distribution of main BGC groups using computational analysis of complete genome sequences of 248 Burkholderia species publicly available. We uncovered significantly differential distribution patterns of BGCs in the Burkholderia phyla, even among strains that are genetically very similar. We found various types of BGCs in Burkholderia, including some representative and most common BGCs for biosynthesis of encrypted or known terpenes, non-ribosomal peptides (NRPs) and some hybrid BGCs for cryptic products. We also observed that Burkholderia contain a lot of unspecified BGCs, representing high potentials to produce novel compounds. Analysis of BGCs for RiPPs (Ribosomally synthesized and posttranslationally modified peptides) and a texobactin-like BGC as examples showed wide classification and diversity of RiPP BGCs in Burkholderia at species level and metabolite predication. In conclusion, as the biggest investigation in silico by far on BGCs of the particular genus Burkholderia, our data implied a great diversity of natural products in Burkholderia and BGC distributions closely related to phylogenetic variation, and suggested different or concurrent strategies used to identify new drug molecules from these microorganisms will be important for the selection of potential BGCs and prolific producing strains for drug discovery.

Molecular and Biochemical Characterization, Antimicrobial Activity, Stress Tolerance, and Plant Growth-Promoting Effect of Endophytic Bacteria Isolated from Wheat Varieties

Endophytic bacteria have been utilized as an alternative source to chemical fertilizers and pesticides to enhance plant productivity and defense mechanisms against biotic and abiotic stress. Five endophytic bacterial strains were isolated from the seeds of three different Pakistani wheat varieties (Ghaneemat-e-IBGE, Atta-Habib, and Siren). The isolated strains AH-1, S-5, S-7, GI-1, and GI-6 showed phylogenetic similarity with Bacillus altitudinis, B. aryabhattai, B. wiedmannii, Pseudomonas aeruginosa, and Burkholderia gladioli, respectively. All strains showed catalase activity (except AH-1) and Indole-3-acetic acid production, with the highest concentration (16.77 μg·mL^-1) found for GI-6, followed by S-5 (11.5 μg·mL^-1), nitrogen assimilation (except S-7), phosphorus solubilization (except S-7 and AH-1), and ability to produce siderophores, with maximum productions for GI-6 (31 ± 3.5 psu) and GI-1 (30 ± 2.9 psu). All five analyzed strains possessed antimicrobial activity, which was particularly strong in GI-6 and S-5 against Klebsiella pneumonia, Escherichia coli, and Bacillus subtilis. Increasing salinity stress with NaCl negatively affected the bacterial growth of all isolates. However, strains GI-6 and S-5 showed salt tolerance after three days of incubation. A drought tolerance test resulted in a negative impact of poly ethylene glycol on bacterial growth, which was, however, less pronounced in GI-6 strain. The GI-6 strain revealed growth-promoting effects on inoculated wheat plants.

MetEx, a Metabolomics Explorer Application for Natural Product Discovery

Advances in next-generation DNA sequencing technologies, bioinformatics, and mass spectrometry-based metabolite detection have ushered in a new era of natural product discovery. Microbial secondary metabolomes are complex, especially when otherwise silent biosynthetic genes are activated, and there is therefore a need for data analysis software to explore and map the resulting multidimensional datasets. To that end, we herein report the Metabolomics Explorer (MetEx), a publicly available web application for the analysis of parallel liquid chromatography-coupled mass spectrometry (LC-MS)-based metabolomics data. MetEx is a highly interactive application that facilitates visualization and analysis of complex metabolomics datasets, consisting of retention time, m/z, and MS intensity features, as a function of hundreds of conditions or elicitors. The software enables prioritization of leads from three-dimensional maps, extraction of two-dimensional slices from various higher order plots, organization of datasets by elicitor chemotypes, customizable library-based dereplication, and automatically scored lead selection. We describe the application of MetEx to the first UPLC-MS-guided high-throughput elicitor screen in which Burkholderia gladioli was challenged with 750 elicitors, and the resulting profiles were interrogated by UPLC-Qtof-MS and subsequently analyzed with the app. We demonstrate the utility of MetEx by reporting elicitors for several cryptic metabolite groups and by uncovering new natural products that remain to be characterized. MetEx is available at https://mo.princeton.edu/MetEx/.

The Hidden Genomic Diversity, Specialized Metabolite Capacity, and Revised Taxonomy of Burkholderia Sensu Lato

Burkholderia sensu lato is a collection of closely related genera within the family Burkholderiaceae that includes species of environmental, industrial, biotechnological, and clinical importance. Multiple species within the complex are the source of diverse specialized metabolites, many of which have been identified through genome mining of their biosynthetic gene clusters (BGCs). However, the full, true genomic diversity of these species and genera, and their biosynthetic capacity have not been investigated. This study sought to cluster and classify over 4000 Burkholderia sensu lato genome assemblies into distinct genomic taxa representing named and uncharacterized species. We delineated 235 species groups by average nucleotide identity analyses that formed seven distinct phylogenomic clades, representing the genera of Burkholderia sensu lato: Burkholderia, Paraburkholderia, Trinickia, Caballeronia, Mycetohabitans, Robbsia, and Pararobbisa. A total of 137 genomic taxa aligned with named species possessing a sequenced type strain, while 93 uncharacterized species groups were demarcated. The 95% ANI threshold proved capable of delineating most genomic species and was only increased to resolve several closely related species. These analyses enabled the assessment of species classifications of over 4000 genomes, and the correction of over 400 genome taxonomic assignments in public databases into existing and uncharacterized genomic species groups. These species groups were genome mined for BGCs, their specialized metabolite capacity calculated per species and genus, and the number of distinct BGCs per species estimated through kmer-based de-replication. Mycetohabitans species dedicated a larger proportion of their relatively small genomes to specialized metabolite biosynthesis, while Burkholderia species harbored more BGCs on average per genome and possessed the most distinct BGCs per species compared to the remaining genera. Exploring the hidden genomic diversity of this important multi-genus complex contributes to our understanding of their taxonomy and evolutionary relationships, and supports future efforts toward natural product discovery.

Total synthesis of the proposed structures of gladiosides I and II

Burkholderia gladioli is a Gram-negative bacterium that biosynthesizes a cocktail of potent antimicrobial compounds, including the antifungal phenolic glycoside sinapigladioside. Herein, we report the total synthesis of the proposed structures of gladiosides I and II, two structurally related phenolic glycosides previously isolated from B. gladioli OR1 cultures. Importantly, the physical and analytical data of the synthetic compounds were in significant discrepancies with the natural products suggesting a misassignment of the originally proposed structures. Furthermore, we have uncovered an acid-catalyzed fragmentation mechanism converting the α,β-unsaturated methyl carbamate-containing gladioside II into the aldehyde-containing gladioside I. Our results lay the foundation for the expeditious synthesis of derivatives of these Burkholderia-derived phenolic glycosides, which would enable to decipher their biological roles and potential pharmacological properties.

Burkholderia in the genomic era: from taxonomy to the discovery of new antimicrobial secondary metabolites

Species of Burkholderia are highly versatile being found not only abundantly in soil, but also as plants and animals' commensals or pathogens. Their complex multireplicon genomes harbour an impressive number of polyketide synthase (PKS) and nonribosomal peptide-synthetase (NRPS) genes coding for the production of antimicrobial secondary metabolites (SMs), which have been successfully deciphered by genome-guided tools. Moreover, genome metrics supported the split of this genus into Burkholderia sensu stricto (s.s.) and five new other genera. Here, we show that the successful antimicrobial SMs producers belong to Burkholderia s.s. Additionally, we reviewed the occurrence, bioactivities, modes of action, structural, and biosynthetic information of thirty-eight Burkholderia antimicrobial SMs shedding light on their diversity, complexity, and uniqueness as well as the importance of genome-guided strategies to facilitate their discovery. Several Burkholderia NRPS and PKS display unusual features, which are reflected in their structural diversity, important bioactivities, and varied modes of action. Up to now, it is possible to observe a general tendency of Burkholderia SMs being more active against fungi. Although the modes of action and biosynthetic gene clusters of many SMs remain unknown, we highlight the potential of Burkholderia SMs as alternatives to fight against new diseases and antibiotic resistance.

The Mechanism of Dehydrating Bimodules in trans-Acyltransferase Polyketide Biosynthesis: A Showcase Study on Hepatoprotective Hangtaimycin

A bioassay‐guided fractionation led to the isolation of hangtaimycin (HTM) from Streptomyces spectabilis CCTCC M2017417 and the discovery of its hepatoprotective properties. Structure elucidation by NMR suggested the need for a structural revision. A putative HTM degradation product was also isolated and its structure was confirmed by total synthesis. The biosynthetic gene cluster was identified and resembles a hybrid trans‐AT PKS/NRPS biosynthetic machinery whose first PKS enzyme contains an internal dehydrating bimodule, which is usually found split in other trans‐AT PKSs. The mechanisms of such dehydrating bimodules have often been proposed, but have never been deeply investigated. Here we present in vivo mutations and in vitro enzymatic experiments that give first and detailed mechanistic insights into catalysis by dehydrating bimodules.

Initiating polyketide biosynthesis by on-line methyl esterification

Aurantinins (ARTs) are antibacterial polyketides featuring a unique 6/7/8/5-fused tetracyclic ring system and a triene side chain with a carboxyl terminus. Here we identify the art gene cluster and dissect ART’s C-methyl incorporation patterns to study its biosynthesis. During this process, an apparently redundant methyltransferase Art28 was characterized as a malonyl-acyl carrier protein O-methyltransferase, which represents an unusual on-line methyl esterification initiation strategy for polyketide biosynthesis. The methyl ester bond introduced by Art28 is kept until the last step of ART biosynthesis, in which it is hydrolyzed by Art9 to convert inactive ART 9B to active ART B. The cryptic reactions catalyzed by Art28 and Art9 represent a protecting group biosynthetic logic to render the ART carboxyl terminus inert to unwanted side reactions and to protect producing organisms from toxic ART intermediates. Further analyses revealed a wide distribution of this initiation strategy for polyketide biosynthesis in various bacteria.

Aurantinins are polyketides with unusual connectivities and broad antibacterial activity. Here the authors show the biosynthesis of aurantinins, which proceeds via an on-line methyl esterification at the terminus that enables the iterative chain elongations prior to condensation and cyclization.

Anti-mycobacterial natural products and mechanisms of action

Covering: up to June, 2020Tuberculosis (TB) continues to be a major disease with high mortality and morbidity globally. Drug resistance and long duration of treatment make antituberculosis drug discovery more challenging. In this review, we summarize recent advances on anti-TB natural products (NPs) and their potential molecular targets in cell wall synthesis, protein production, energy generation, nucleic acid synthesis and other emerging areas. We highlight compounds with activity against drug-resistant TB, and reveal several novel targets including Mtb biotin synthase, ATP synthase, 1,4-dihydroxy-2-naphthoate prenyltransferase and biofilms. These anti-TB NPs and their targets could facilitate target-based screening and accelerate TB drug discovery.

Drug discovery through the isolation of natural products from Burkholderia

Introduction: The increasing threat of antibiotic-resistant pathogens makes it imperative that new antibiotics to combat them are discovered. Burkholderia is a genus of Gram-negative, non-sporulating bacteria. While ubiquitous and capable of growing within plants and groundwater, they are primarily soil-dwelling organisms. These include the more virulent forms of Burkholderia such as Burkholderia mallei, Burkholderia pseudomallei, and the Burkholderia cepacia complex (Bcc).Areas covered: This review provides a synopsis of current research on the natural products isolated from the genus Burkholderia. The authors also cover the research on the drug discovery efforts that have been performed on the natural products derived from Burkholderia.Expert opinion: Though Burkholderia has a small number of pathogenic species, the majority of the genus is avirulent and almost all members of the genus are capable of producing useful antimicrobial products that could potentially lead to the development of novel therapeutics against infectious diseases. The need for discovery of new antibiotics is urgent due to the ever-increasing prevalence of antibiotic-resistant pathogens, coupled with the decline in the discovery of new antibiotics.

Combining NMR-Based Metabolic Profiling and Genome Mining for the Accelerated Discovery of Archangiumide, an Allenic Macrolide from the Myxobacterium Archangium violaceum SDU8

An unprecedented 19-membered allenic macrolide archangiumide (1) was discovered from the myxobacterium Archangium violaceum SDU8 by integrating NMR-based metabolic profiling and genome mining. Its biosynthesis pathway was proposed based on the architectural analysis of the encoding trans-AT PKS genes and validated by isotope labeling. The methodology of combing 2D NMR-based metabolic profiling and bioinformatics-aided structure prediction, as exemplified by this study, is anticipated to improve discovery efficiency of a broader range of microbial "dark matter".

Discovery of a Novel Lineage Burkholderia cepacia ST 1870 Endophytically Isolated from Medicinal Polygala paniculata Which Shows Potent In Vitro Antileishmanial and Antimicrobial Effects

In this study, we report the isolation and identification of an endophytic strain of Burkholderia cepacia (COPS strain) associated with Polygala paniculata roots. Polygala plants are rich sources of promising microbiomes, of which the literature reports several pharmacological effects, such as trypanocidal, antinociceptive, anesthetic, anxiolytics, and anticonvulsant activities. B. cepacia COPS belongs to a new sequence type (ST 1870) and harbors a genome estimated in 8.3 Mbp which exhibits the aminoglycosides and beta-lactams resistance genes aph(3′)-IIa and bla_TEM-116, respectively. Analysis performed using MLST, average nucleotide identity, and digital DNA-DNA hybridization support its species-level identification and reveals its novel housekeeping genes alleles gyrB, lepA, and phaC. The root endophyte B. cepacia COPS drew our attention from a group of 14 bacterial isolates during the primary screening for being potentially active against Staphylococcus aureus ATCC 29213, Enterococcus faecalis ATCC 29212, Micrococcus luteus ATCC 9341, Escherichia coli ATCC 25922, and Candida albicans ATCC 10231 and exhibited the broad-spectrum activity against phytopathogenic fungi. In addition, COPS strain showed production of protease, lipase, and esterase in solid media, and its natural product extract showed potent inhibition against fungal plant pathogens, such as Moniliophthora perniciosa, whose antagonism index (89.32%) exceeded the positive control (74.17%), whereas Sclerotinia sclerotiorum and Ceratocystis paradoxa showed high percentages of inhibition (85.53% and 82.69%, respectively). COPS crude extract also significantly inhibited S. epidermidis ATCC 35984, E. faecium ATCC 700221 (MIC values of 32 μg/mL for both), E. faecalis ATCC 29212 (64 μg/mL), and S. aureus ATCC 25923 (128 μg/mL). We observed moderate antagonistic activity against A. baumannii ATCC 19606 and E. coli ATCC 25922 (both at 512 μg/mL), as well as potent cytotoxic effects on Leishmania infantum and Leishmania major promastigote forms with 78.25% and 57.30% inhibition. In conclusion, this study presents for the first time the isolation of an endophytic B. cepacia strain associated with P. paniculata and enough evidence that these plants may be considered a rich source of microbes for the fight against neglected diseases.

Burkholderia Bacteria Produce Multiple Potentially Novel Molecules that Inhibit Carbapenem-Resistant Gram-Negative Bacterial Pathogens

Antimicrobial resistance in Gram-negative pathogens represents a global threat to human health. This study determines the antimicrobial potential of a taxonomically and geographically diverse collection of 263 Burkholderia (sensu lato) isolates and applies natural product dereplication strategies to identify potentially novel molecules. Antimicrobial activity is almost exclusively present in Burkholderia sensu stricto bacteria and rarely observed in the novel genera Paraburkholderia, Caballeronia, Robbsia, Trinickia, and Mycetohabitans. Fourteen isolates show a unique spectrum of antimicrobial activity and inhibited carbapenem-resistant Gram-negative bacterial pathogens. Dereplication of the molecules present in crude spent agar extracts identifies 42 specialized metabolites, 19 of which represented potentially novel molecules. The known identified Burkholderia metabolites include toxoflavin, reumycin, pyrrolnitrin, enacyloxin, bactobolin, cepacidin, ditropolonyl sulfide, and antibiotics BN-227-F and SF 2420B, as well as the siderophores ornibactin, pyochelin, and cepabactin. Following semipreparative fractionation and activity testing, a total of five potentially novel molecules are detected in active fractions. Given the molecular formula and UV spectrum, two of those putative novel molecules are likely related to bactobolins, and another is likely related to enacyloxins. The results from this study confirm and extend the observation that Burkholderia bacteria present exciting opportunities for the discovery of potentially novel bioactive molecules.

Genomics-Driven Activation of Silent Biosynthetic Gene Clusters in Burkholderia gladioli by Screening Recombineering System

The Burkholderia genus possesses ecological and metabolic diversities. A large number of silent biosynthetic gene clusters (BGCs) in the Burkholderia genome remain uncharacterized and represent a promising resource for new natural product discovery. However, exploitation of the metabolomic potential of Burkholderia is limited by the absence of efficient genetic manipulation tools. Here, we screened a bacteriophage recombinase system Redγ-BAS, which was functional for genome modification in the plant pathogen Burkholderia gladioli ATCC 10248. By using this recombineering tool, the constitutive promoters were precisely inserted in the genome, leading to activation of two silent nonribosomal peptide synthetase gene clusters (bgdd and hgdd) and production of corresponding new classes of lipopeptides, burriogladiodins A–H (1–8) and haereogladiodins A–B (9–10). Structure elucidation revealed an unnatural amino acid Z- dehydrobutyrine (Dhb) in 1–8 and an E-Dhb in 9–10. Notably, compounds 2–4 and 9 feature an unusual threonine tag that is longer than the predicted collinearity assembly lines. The structural diversity of burriogladiodins was derived from the relaxed substrate specificity of the fifth adenylation domain as well as chain termination conducted by water or threonine. The recombinase-mediating genome editing system is not only applicable in B. gladioli, but also possesses great potential for mining meaningful silent gene clusters from other Burkholderia species.

The In Vitro and In Planta Interspecies Interactions Among Rice-Pathogenic Burkholderia Species

Burkholderia glumae, B. plantarii, and B. gladioli are responsible for serious diseases in rice crops and co-occurrence among them has been reported. In this study, in vitro assays revealed antagonistic activity among these organisms, with B. gladioli demonstrating strong inhibition of B. glumae and B. plantarii. Strains of B. glumae and B. plantarii that express green fluorescent protein were constructed and used for cocultivation assays with B. gladioli, which confirmed the strong inhibitory activity of B. gladioli. Cell-free supernatants from each species were tested against cultures of counterpart species to evaluate the potential to inhibit bacterial growth. To investigate the inhibitory activity of B. gladioli on B. glumae and B. plantarii in rice, rice plant assays were performed and quantitative PCR (qPCR) assays were developed for in planta bacterial quantification. The results indicated that coinoculation with B. gladioli leads to significantly reduced disease severity and colonization of rice tissues compared with single inoculation with B. glumae or B. plantarii. This study demonstrates the interactions among three rice-pathogenic Burkholderia species and strong antagonistic activity of B. gladioli in vitro and in planta. The qPCR assays developed here could be applied for accurate quantification of these organisms from in planta samples in future studies.

Kill and cure: genomic phylogeny and bioactivity of Burkholderia gladioli bacteria capable of pathogenic and beneficial lifestyles

Burkholderia gladioli is a bacterium with a broad ecology spanning disease in humans, animals and plants, but also encompassing multiple beneficial interactions. It is a plant pathogen, a toxin-producing food-poisoning agent, and causes lung infections in people with cystic fibrosis (CF). Contrasting beneficial traits include antifungal production exploited by insects to protect their eggs, plant protective abilities and antibiotic biosynthesis. We explored the genomic diversity and specialized metabolic potential of 206 B. gladioli strains, phylogenomically defining 5 clades. Historical disease pathovars (pv.) B. gladioli pv. allicola and B. gladioli pv. cocovenenans were distinct, while B. gladioli pv. gladioli and B. gladioli pv. agaricicola were indistinguishable; soft-rot disease and CF infection were conserved across all pathovars. Biosynthetic gene clusters (BGCs) for toxoflavin, caryoynencin and enacyloxin were dispersed across B. gladioli, but bongkrekic acid and gladiolin production were clade-specific. Strikingly, 13 % of CF infection strains characterized were bongkrekic acid-positive, uniquely linking this food-poisoning toxin to this aspect of B. gladioli disease. Mapping the population biology and metabolite production of B. gladioli has shed light on its diverse ecology, and by demonstrating that the antibiotic trimethoprim suppresses bongkrekic acid production, a potential therapeutic strategy to minimize poisoning risk in CF has been identified.

Polyketide β-branching: diversity, mechanism and selectivity

Covering: 2008 to August 2020 Polyketides are a family of natural products constructed from simple building blocks to generate a diverse range of often complex chemical structures with biological activities of both pharmaceutical and agrochemical importance. Their biosynthesis is controlled by polyketide synthases (PKSs) which catalyse the condensation of thioesters to assemble a functionalised linear carbon chain. Alkyl-branches may be installed at the nucleophilic α- or electrophilic β-carbon of the growing chain. Polyketide β-branching is a fascinating biosynthetic modification that allows for the conversion of a β-ketone into a β-alkyl group or functionalised side-chain. The overall transformation is catalysed by a multi-protein 3-hydroxy-3-methylglutaryl synthase (HMGS) cassette and is reminiscent of the mevalonate pathway in terpene biosynthesis. The first step most commonly involves the aldol addition of acetate to the electrophilic carbon of the β-ketothioester catalysed by a 3-hydroxy-3-methylglutaryl synthase (HMGS). Subsequent dehydration and decarboxylation selectively generates either α,β- or β,γ-unsaturated β-alkyl branches which may be further modified. This review covers 2008 to August 2020 and summarises the diversity of β-branch incorporation and the mechanistic details of each catalytic step. This is extended to discussion of polyketides containing multiple β-branches and the selectivity exerted by the PKS to ensure β-branching fidelity. Finally, the application of HMGS in data mining, additional β-branching mechanisms and current knowledge of the role of β-branches in this important class of biologically active natural products is discussed.

Burkholderia gladioli CGB10: A Novel Strain Biocontrolling the Sugarcane Smut Disease

In this study, we isolated an endophytic Burkholderia gladioli strain, named CGB10, from sugarcane leaves. B. gladioli CGB10 displayed strong inhibitory activity against filamentous growth of fungal pathogens, one of which is Sporisorium scitamineum that causes sugarcane smut, a major disease affecting the quality and production of sugarcane in tropical and subtropical regions. CGB10 could effectively suppress sugarcane smut under field conditions, without itself causing any obvious damage or disease, thus underscoring a great potential as a biocontrol agent (BCA) for the management of sugarcane smut. A toxoflavin biosynthesis and transport gene cluster potentially responsible for such antifungal activity was identified in the CGB10 genome. Additionally, a quorum-sensing gene cluster was identified too and compared with two close Burkholderia species, thus supporting an overall connection to the regulation of toxoflavin synthesis therein. Overall, this work describes the in vitro and field Sporisorium scitamineum biocontrol by a new B. gladioli strain, and reports genes and molecular mechanisms potentially involved.

Discovery and Biosynthesis of Bolagladins: Unusual Lipodepsipeptides from Burkholderia gladioli Clinical Isolates*

Two Burkholderia gladioli strains isolated from the lungs of cystic fibrosis patients were found to produce unusual lipodepsipeptides containing a unique citrate-derived fatty acid and a rare dehydro-β-alanine residue. The gene cluster responsible for their biosynthesis was identified by bioinformatics and insertional mutagenesis. In-frame deletions and enzyme activity assays were used to investigate the functions of several proteins encoded by the biosynthetic gene cluster, which was found in the genomes of about 45 % of B. gladioli isolates, suggesting that its metabolic products play an important role in the growth and/or survival of the species. The Chrome Azurol S assay indicated that these metabolites bind ferric iron, which suppresses their production when added to the growth medium. Moreover, a gene encoding a TonB-dependent ferric-siderophore receptor is adjacent to the biosynthetic genes, suggesting that these metabolites may function as siderophores in B. gladioli.

Advances in antibiotic drug discovery: reducing the barriers for antibiotic development

Antibiotic drug discovery has been an essential field of research since the early 1900s, but the threat from infectious bacteria has only increased over the decades because of the emergence of widespread multidrug resistance. In this review, we discuss the recent advances in natural product, computational and medicinal chemistry that have reinvigorated the field of antibiotic drug discovery while giving perspective on how easily, both in cost and in expertise, these methods can be implemented by other researchers with the goal of increasing the number of scientists contributing to this public health crisis.

Genomics-Driven Discovery of a Novel Glutarimide Antibiotic from Burkholderia gladioli Reveals an Unusual Polyketide Synthase Chain Release Mechanism

A gene cluster encoding a cryptic trans‐acyl transferase polyketide synthase (PKS) was identified in the genomes of Burkholderia gladioli BCC0238 and BCC1622, both isolated from the lungs of cystic fibrosis patients. Bioinfomatics analyses indicated the PKS assembles a novel member of the glutarimide class of antibiotics, hitherto only isolated from Streptomyces species. Screening of a range of growth parameters led to the identification of gladiostatin, the metabolic product of the PKS. NMR spectroscopic analysis revealed that gladiostatin, which has promising activity against several human cancer cell lines and inhibits tumor cell migration, contains an unusual 2‐acyl‐4‐hydroxy‐3‐methylbutenolide in addition to the glutarimide pharmacophore. An AfsA‐like domain at the C‐terminus of the PKS was shown to catalyze condensation of 3‐ketothioesters with dihydroxyacetone phosphate, thus indicating it plays a key role in polyketide chain release and butenolide formation.

Antimicrobial activity of enacyloxin IIa and gladiolin against the urogenital pathogens Neisseria gonorrhoeae and Ureaplasma spp

AIMS

To determine the antimicrobial activity of enacyloxin IIa and gladiolin against Neisseria gonorrhoeae and Ureaplasma spp.

METHODS AND RESULTS

The Burkholderia polyketide antibiotics enacyloxin IIa and gladiolin were tested against 14 N. gonorrhoeae and 10 Ureaplasma spp. isolates including multidrug-resistant N. gonorrhoeae isolates WHO V, WHO X and WHO Z as well as macrolide, tetracycline and ciprofloxacin-resistant ureaplasmas. Susceptibility testing of N. gonorrhoeae was carried out by agar dilution, whereas broth micro-dilution and growth kinetic assays were used for Ureaplasma spp. The MIC range for enacyloxin IIa and gladiolin against N. gonorrhoeae was 0·015-0·06 mg l^-1 and 1-2 mg l^-1 respectively. The presence of resistance to front line antibiotics had no effect on MIC values. The MIC range for enacyloxin IIa against Ureaplasma spp. was 4-32 mg l^-1 with a clear dose-dependent effect when observed using a growth kinetic assay. Gladiolin had no antimicrobial activity on Ureaplasma spp. at 32 mg l^-1 and limited impact on growth kinetics.

CONCLUSIONS

Enacyloxin IIa and gladiolin antibiotics have antimicrobial activity against a range of antibiotic susceptible and resistant N. gonorrhoeae and Ureaplasma isolates.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study highlights the potential for a new class of antimicrobial against pathogens in which limited antibiotics are available. Development of these compounds warrants further investigation in the face of emerging extensively drug-resistant strains.

Unlocking Cryptic Metabolites with Mass Spectrometry-Guided Transposon Mutant Selection

The products of most secondary metabolite biosynthetic gene clusters (BGCs) have yet to be discovered, in part due to low expression levels in laboratory cultures. Reporter-guided mutant selection (RGMS) has recently been developed for this purpose: a mutant library is generated and screened, using genetic reporters to a chosen BGC, to select transcriptionally active mutants that then enable the characterization of the "cryptic" metabolite. The requirement for genetic reporters limits the approach to a single pathway within genetically tractable microorganisms. Herein, we utilize untargeted metabolomics in conjunction with transposon mutagenesis to provide a global read-out of secondary metabolism across large numbers of mutants. We employ self-organizing map analytics and imaging mass spectrometry to identify and characterize seven cryptic metabolites from mutant libraries of two different Burkholderia species. Applications of the methodologies reported can expand our understanding of the products and regulation of cryptic BGCs across phylogenetically diverse bacteria.

Genomic Assemblies of Members of Burkholderia and Related Genera as a Resource for Natural Product Discovery

The genomes of 450 members of Burkholderiaceae, isolated from clinical and environmental sources, were sequenced and assembled as a resource for genome mining. Genomic analysis of the collection has enabled the identification of multiple metabolites and their biosynthetic gene clusters, including the antibiotics gladiolin, icosalide A, enacyloxin, and cepacin A.

The genomes of 450 members of Burkholderiaceae, isolated from clinical and environmental sources, were sequenced and assembled as a resource for genome mining. Genomic analysis of the collection has enabled the identification of multiple metabolites and their biosynthetic gene clusters, including the antibiotics gladiolin, icosalide A, enacyloxin, and cepacin A.

A rapid screening method for the detection of specialised metabolites from bacteria: Induction and suppression of metabolites from Burkholderia species

Screening microbial cultures for specialised metabolites is essential for the discovery of new biologically active compounds. A novel, cost-effective and rapid screening method is described for extracting specialised metabolites from bacteria grown on agar plates, coupled with HPLC for basic identification of known and potentially novel metabolites. The method allows the screening of culture collections to identify optimal production strains and metabolite induction conditions. The protocol was optimised on two Burkholderia species known to produce the antibiotics, enacyloxin IIa (B. ambifaria) and gladiolin (B. gladioli), respectively; it was then applied to strains of each species to identify high antibiotic producers. B. ambifaria AMMD and B. gladioli BCC0238 produced the highest concentrations of the respective antibiotic under the conditions tested. To induce expression of silent biosynthetic gene clusters, the addition of low concentrations of antibiotics to growth media was evaluated as known elicitors of Burkholderia specialised metabolites. Subinhibitory concentrations of trimethoprim and other clinically therapeutic antibiotics were evaluated and screened against a panel of B. gladioli and B. ambifaria. To enhance rapid strain screening with more antibiotic elicitors, antimicrobial susceptibility testing discs were included within the induction medium. Low concentrations of trimethoprim suppressed the production of specialised metabolites in B. gladioli, including the toxins, toxoflavin and bongkrekic acid. However, the addition of trimethoprim significantly improved enacylocin IIa concentrations in B. ambifaria AMMD. Rifampicin and ceftazidime significantly improved the yield of gladiolin and caryoynencin by B. gladioli BCC0238, respectively, and cepacin increased 2-fold with tobramycin in B. ambifaria BCC0191. Potentially novel metabolites were also induced by subinhibitory concentrations of tobramycin and chloramphenicol in B. ambifaria. In contrast to previous findings that low concentrations of antibiotic elicit Burkholderia metabolite production, we found they acted as both inducers or suppressors dependent on the metabolite and the strains producing them. In conclusion, the screening protocol enabled rapid characterization of Burkholderia metabolites, the identification of suitable producer strains, potentially novel natural products and an understanding of metabolite regulation in the presence of inducing or suppressing conditions.

Regulation of Virulence by Two-Component Systems in Pathogenic Burkholderia

The regulation and timely expression of bacterial genes during infection is critical for a pathogen to cause an infection. Bacteria have multiple mechanisms to regulate gene expression in response to their environment, one of which is two-component systems (TCS). TCS have two components. One component is a sensory histidine kinase (HK) that autophosphorylates when activated by a signal. The activated sensory histidine kinase then transfers the phosphoryl group to the second component, the response regulator, which activates transcription of target genes. The genus Burkholderia contains members that cause human disease and are often extensively resistant to many antibiotics. The Burkholderia cepacia complex (BCC) can cause severe lung infections in patients with cystic fibrosis (CF) or chronic granulomatous disease (CGD). BCC members have also recently been associated with several outbreaks of bacteremia from contaminated pharmaceutical products. Separate from the BCC is Burkholderia pseudomallei, which is the causative agent of melioidosis, a serious disease that occurs in the tropics, and a potential bioterrorism weapon. Bioinformatic analysis of sequenced Burkholderia isolates predicts that most strains have at least 40 TCS. The vast majority of these TCS are uncharacterized both in terms of the signals that activate them and the genes that are regulated by them. This review will highlight TCS that have been described to play a role in virulence in either the BCC or B. pseudomallei Since many of these TCS are involved in virulence, TCS are potential novel therapeutic targets, and elucidating their function is critical for understanding Burkholderia pathogenesis.

The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential

Three strains of fungus-associated Burkholderiales bacteria with antagonistic activity against Gram-negative plant pathogens were genome sequenced to investigate their taxonomic placement and potential for antimicrobial specialized metabolite production. The selected strains were identified as novel taxa belonging to the genus Paraburkholderia and carry multiple biosynthetic gene clusters.