Generation and screening of natural product-like compounds for antibiotic discovery

Avec l’apparition de plus en plus de souches de bactérie résistante aux antibiotiques, le développement de nouveaux antibiotiques est devenu une important problématique pour les agences de santé. C’est pour cela que la création de nouvelles plateformes pour accélérer la découverte de médicaments est devenu un besoin urgent. Dans les dernières décennies, la recherche était principalement orientée sur la modification de molécules préexistantes, la méta-analyse d’organismes produisant des molécules activent et l’analyse de librairies moléculaires pour trouver des molécules synthétiques activent, ce qui s’est avéré relativement inefficace. Notre but était donc de développer de nouvelles molécules avec des effets thérapeutiques de façon plus efficace à une fraction du prix et du temps comparé à ce qui se fait actuellement. Comme structure de base, nous avons utilisé des métabolites secondaires qui pouvaient altérer le fonctionnement des protéines ou l’interaction entre deux protéines. Pour générer ces molécules, j’ai concentré mes efforts sur les terpènes, une classe de métabolites secondaires qui possède un large éventail d’activités biologiques incluant des activités antibactériennes. Nous avons développé un système de chromosome artificiel de levure (YAC) qui permet à la fois l’assemblage directionnel et combinatoire de gènes qui permet la création de voies de biosynthèse artificielles. Comme preuve de concept, j’ai développé des YACs qui contiennent les gènes pour l’expression des enzymes impliquées dans la biosynthèse de la -carotène et de l’albaflavenone et produit ces molécules avec un haut rendement. Finalement, Des YACs produits à partir de librairies de gènes ont permis de créer une grande diversité de molécules.With the appearance of more and more antibiotic resistant strains of bacteria, the development of new antibiotics becomes an issue of utmost importance for society. It is for that reason that new platforms and methodologies to accelerate the discovery of novel antibiotics are urgently needed. For the last decades, research was mainly oriented on modifying existing antibiotics, mining natural producers or screening for synthetic molecules from giant chemical libraries but these approaches did not manage to keep the pipelines filled with a sufficient number of novel antibiotics. Therefore, our goal was to develop a way to create and screen new molecules more efficiently at a fraction of the cost when compared to traditional approaches and within a short time frame. As chemical scaffolds we use natural product-like compounds that modulate the function of individual proteins or of protein-protein interactions. To generate these compounds, I focused first on the terpene scaffold class, a class containing molecules with a wide range of biological activities and includes compounds with antibacterial activities. We developed a yeast artificial chromosome (YAC) platform that allows both directional and combinatorial assembly of biosynthetic genes that can be used to create artificial biosynthetic pathways. As a proof of principle, YACs were successfully assembled containing genes coding for enzymes involved in the biosynthesis of both B-carotene and albaflavenone, and that allowed high yield production of these compounds. Finally, YACs encoding terpene gene libraries were also created and which produced a diversity of terpenoid molecules

Recent Developments in Selected Sesquiterpenes: Molecular Rearrangements, Biosynthesis, and Structural Relationship among Congeners

Recent developments in selected sesquiterpenoids are reviewed for the past one decade (2005–2017) with special reference to Mechanisms of multistep molecular rearrangements of some sesquiterpenes or derivatives based on isotopic labeling studies and extensive spectroscopic analysis such as molecular rearrangement of acetyl cedrene to cedrene follower, acid catalyzed rearrangement of moreliane-based triketone, synthesis of (−)-isocomene and (−)-triquinane by acid-catalyzed rearrangement of (−)-modhephene, Total synthesis of (+)-cymbodiacetal, BF3 catalyzed molecular rearrangements of mono epoxides of α- and β-himachalenes, santonic acid: Zn-HCl-ether reduction. Insights into biosynthesis of albaflavenone, caryol-1(11)-ene-10-ol, (+)-koraiol, pogostol, patchouli alcohol and valerenadiene are discussed. Congeners for probing structure-biosynthetic relationship. This approach is discussed with the availability of very interesting results on the isolation of highly oxygenated secondary metabolites from endophytic fungi, Xylaria sp

Prospecting Novel Microbiomes for Antibiotic Compounds using Metagenomics and Genome Mining

There has been a void in the discovery and development of new antibiotic classes over the past four decades due, in part, to the traditional bioprospecting pipeline becoming inefficient from high compound rediscovery rates and high costs. The need for new antibiotic classes is urgent as antimicrobial drug resistant infections are now a major public health concern. Strategies such as exploring novel environments, use of next-generation sequencing, and metagenomics may reduce rediscovery rates and costs which could help accelerate lead discovery and encourage greater participation in bioprospecting. Whole genome-sequencing and analysis was used to characterise four bacterial strains (Y1-4) isolated from raw honey that were shown to have antibiotic activity. The isolates were identified as Bacillus and were closely related but distinctive strains with variations amongst their secondary metabolite profiles. All isolates contained a gene cluster homologous to AS- 48, a circular bacteriocin produced by Enterococcus faecalis, which has broad-spectrum antibiotic activity. To date, no example of this bacteriocin has been reported in Bacillus. This work demonstrated the value of whole-microbial genome sequencing for dereplication. A pipeline for the low-cost sequencing and assembly of bacterial genomes using Oxford Nanopore MinION was developed in order to produce contiguous and accurate genome assemblies for taxonomic and bioprospecting analysis. The pipeline developed used a combination of Nanopore draft assembly by Canu and polishing with RACON and Nanopolish, with final polishing with Illumina reads using Pilon. The Nanopore-only assembly of Streptomyces coelicolor A3(2) produced was contiguous and covered 98.9 % of reference. AntiSMASH analysis identified the full secondary metabolite profile of the genome through homology searches. However, indel rates were high (66.82 per 100 kbp) causing fragmented gene annotations which limited secondary metabolite structure prediction. Illumina read polishing reduced indels (2.03 per 100 kbp) and enabled accurate structure prediction from the identified biosynthetic pathways. This demonstrates that Nanopore sequencing can provide a viable dereplication strategy by detection of known biosynthetic pathways. Additionally, supplementation with Illumina sequencing can allow for structure prediction of biosynthetic pathways which could inform chemical extraction strategies for novel pathways. Nanopore sequencing was further utilised to characterise an antibiotic producing isolate (KB16) active against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus from the hot spring of the Roman Baths, UK. Genomic analysis showed KB16 to be highly related to Streptomyces canus and to contain 26 putative secondary metabolite gene clusters - some of which were potentially novel. One of the gene clusters was identified as encoding the antibiotic albaflavenone. Attempts to chemically identify the antibiotic produced by KB16 showed that it may produce multiple antimicrobial compounds. These findings demonstrate the value in prospecting underexplored environments such as the Roman Baths for microbially-derived antimicrobial leads. A PCR screen was used to amplify NRPS and PKS gene fragments from a human oral metagenome. Analysis of the fragments suggested that some are from uncharacterised gene clusters. Nanopore shotgun metagenomic sequencing was used to profile the water of the Roman Baths which revealed a diverse microbiome of species with reported metabolic characteristics that are in keeping with the known geochemistry of the waters and aligned with 16S rRNA analysis. Further analysis also identified putative heavy metal resistance genes which can be a co-marker for their metabolism and aligned with the chemical properties of the water. These findings demonstrate the potential value in these sites for bioprospecting whilst also giving insight that can inform bioprospecting strategies. The investigations also highlight the utility of Nanopore sequencing for taxonomic and functional gene profiling of environmental microbiomes. In combination these findings have all contributed information on novel environments, potential isolate leads, and cost-efficient methodologies to accelerate the discovery of microbially-derived antibiotics

Complete genome sequence of Streptomyces formicae KY5, the formicamycin producer

Here we report the complete genome of the new species Streptomyces formicae KY5 isolated from Tetraponera fungus growing ants. S. formicae was sequenced using the PacBio and 454 platforms to generate a single linear chromosome with terminal inverted repeats. Illumina MiSeq sequencing was used to correct base changes resulting from the high error rate associated with PacBio. The genome is 9.6 Mbps, has a GC content of 71.38% and contains 8162 protein coding sequences. Predictive analysis shows this strain encodes at least 45 gene clusters for the biosynthesis of secondary metabolites, including a type 2 polyketide synthase encoding cluster for the antibacterial formicamycins. Streptomyces formicae KY5 is a new, taxonomically distinct Streptomyces species and this complete genome sequence provides an important marker in the genus of Streptomyces

Mining microbial genomes for new natural products and biosynthetic pathways

Analyses of microbial genome sequences have revealed numerous examples of ‘cryptic’ or ‘orphan’ biosynthetic gene clusters, with the potential to direct the production of novel, structurally complex natural products. This article summarizes the various methods that have been developed for discovering the products of cryptic biosynthetic gene clusters in microbes and gives an account of my group's discovery of the products of two such gene clusters in the model actinomycete Streptomyces coelicolor M145. These discoveries hint at new mechanisms, roles and specificities for natural product biosynthetic enzymes. Our efforts to elucidate these are described. The identification of new secondary metabolites of S. coelicolor raises the question: what is their biological function? Progress towards answering this question is also summarized

Comparative Genomics Reveals Prophylactic and Catabolic Capabilities of Actinobacteria within the Fungus-Farming Termite Symbiosis

Actinobacteria, one of the largest bacterial phyla, are ubiquitous in many of Earth’s ecosystems and often act as defensive symbionts with animal hosts. Members of the phylum have repeatedly been isolated from basidiomycete-cultivating fungus-farming termites that maintain a monoculture fungus crop on macerated dead plant substrate. The proclivity for antimicrobial and enzyme production of Actinobacteria make them likely contributors to plant decomposition and defense in the symbiosis. To test this, we analyzed the prophylactic (biosynthetic gene cluster [BGC]) and metabolic (carbohydrate-active enzyme [CAZy]) potential in 16 (10 existing and six new genomes) termite-associated Actinobacteria and compared these to the soil-dwelling close relatives. Using antiSMASH, we identified 435 BGCs, of which 329 (65 unique) were similar to known compound gene clusters, while 106 were putatively novel, suggesting ample prospects for novel compound discovery. BGCs were identified among all major compound categories, including 26 encoding the production of known antimicrobial compounds, which ranged in activity (antibacterial being most prevalent) and modes of action that might suggest broad defensive potential. Peptide pattern recognition analysis revealed 823 (43 unique) CAZymes coding for enzymes that target key plant and fungal cell wall components (predominantly chitin, cellulose, and hemicellulose), confirming a substantial degradative potential of these bacteria. Comparison of termite-associated and soil-dwelling bacteria indicated no significant difference in either BGC or CAZy potential, suggesting that the farming termite hosts may have coopted these soil-dwelling bacteria due to their metabolic potential but that they have not been subject to genome change associated with symbiosis. IMPORTANCE Actinobacteria have repeatedly been isolated in fungus-farming termites, and our genome analyses provide insights into the potential roles they may serve in defense and for plant biomass breakdown. These insights, combined with their relatively higher abundances in fungus combs than in termite gut, suggest that they are more likely to play roles in fungus combs than in termite guts. Up to 25% of the BGCs we identify have no similarity to known clusters, indicating a large potential for novel chemistry to be discovered. Similarities in metabolic potential of soil-dwelling and termite-associated bacteria suggest that they have environmental origins, but their consistent presence with the termite system suggests their importance for the symbiosis

Modulation of multiple gene clusters’ expression by the PAS-LuxR transcriptional regulator PteF

[EN] PAS-LuxR transcriptional regulators are conserved proteins governing polyene antifungal biosynthesis. PteF is the regulator of filipin biosynthesis from Streptomyces avermitilis. Its mutation drastically abates filipin, but also oligomycin production, a macrolide ATP-synthase inhibitor, and delays sporulation; thus, it has been considered a transcriptional activator. Transcriptomic analyses were performed in S. avermitilis ΔpteF and its parental strain. Both strains were grown in a YEME medium without sucrose, and the samples were taken at exponential and stationary growth phases. A total of 257 genes showed an altered expression in the mutant, most of them at the exponential growth phase. Surprisingly, despite PteF being considered an activator, most of the genes affected showed overexpression, thereby suggesting a negative modulation. The affected genes were related to various metabolic processes, including genetic information processing; DNA, energy, carbohydrate, and lipid metabolism; morphological differentiation; and transcriptional regulation, among others, but were particularly related to secondary metabolite biosynthesis. Notably, 10 secondary metabolite gene clusters out of the 38 encoded by the genome showed altered expression profiles in the mutant, suggesting a regulatory role for PteF that is wider than expected. The transcriptomic results were validated by quantitative reverse-transcription polymerase chain reaction. These findings provide important clues to understanding the intertwined regulatory machinery that modulates antibiotic biosynthesis in StreptomycesSIThis research was funded by the Spanish Ministerio de Economía, Industria y Competitividad (grants BIO2013-42983-P and PCIN-2016-190 to J.F.A.), FPU contracts of the Ministerio de Educación, Cultura y Deporte (AP2007-02055 to T.D.P., FPU13/01537 to A.d.P.), a contract from the Junta de Castilla y León co-financed by the European Social Fund (to E.G.B.), and a fellowship from the Portuguese Fundação para a Ciência e a Tecnologia (SFRH/BD/64006/2009 to C.M.V.)

Exploitation of underused Streptomyces through a combined metabolomics-genomics workflow to enhance natural product diversity.

The genus Streptomyces is the source of approximately two-thirds of all clinically-used antibiotics. Despite being the source of so many specialised metabolites, genomic analysis indicates that most Streptomyces strains have the potential to produce around twenty-five bioactive metabolites, some of which may be the basis of novel therapies. This makes culture collections of Streptomyces spp. an easily accessible (but under-used) resource to mine for genomic and metabolomic variety. Therefore, the main aim of this project was to initiate exploitation of the culture collection at NCIMB Ltd., by expanding the available chemical space from under-utilised Streptomyces for the production of novel antibiotics. This primarily used a mixture of metabolomic and genomic methods. A high-throughput culture parameter screen was designed around multiple carbon sources, nitrogen sources and extraction sample times. This was tested on the model species S. coelicolor A3(2) to compare differences in the production of known specialised metabolites, using UPLC-MS to analyse crude extracts from growth on agar. Data was analysed using MZmine and putative metabolites were identified using freely-available MS/MS databases - primarily GNPS. This showed clear variation in production of nine identified metabolites - including deferoxamines, germicidins, undecylprodigiosin and coelichelin - as a result of different culture parameters. Therefore, the screen successfully expanded the available chemical space, so was applied to non-model Streptomyces strains. The screen was used to compare the total metabolomic variety produced by three Streptomyces, isolated from different environments, in order to select a strain for further investigation. Comparing metabolomic features using principal component analysis showed the Costa Rican soil isolate S. costaricanus to produce the most variety versus the other two Streptomyces strains. The metabolite family most responsible for principal component separation was identified as the actinomycins. Scale-up of both agar and broth culture was used for metabolite dereplication and bioassays against multidrug resistant Acinetobacter baumannii, which is one of the bacteria on the World Health Organisation's list of pathogens that most urgently require new therapies. Fractions were derived from broth culture supernatant and agar crude extract by flash chromatography, resulting in semi-purified fractions. The predominant metabolite families in fractions were actinomycins and deferoxamines, which were further split by polarity into separate fractions. This resulted in rapid purification of metabolites, with one fraction comprising 80% deferoxamine B by weight. Fractions were tested against A. baumannii using the 2,3-bis (2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino)carbonyl]-2H-tetrazolium hydroxide (XTT) assay, which showed partial inhibition of growth at 50 µg/ml. Examining the bioactive fractions showed potentially novel minor peaks that could be responsible for bioactivity. A high-quality full genome of S. costaricanus was obtained using a combination of MiSeq and MinION sequences. This was analysed with RAST and antiSMASH to determine the specialised metabolite potential of S. costaricanus. AntiSMASH detected thirty-three biosynthetic gene clusters (BGCs), above the mean for Streptomyces. Thus, the confirmed genomic potential also suggested a wider metabolite variety, as indicated by the metabolomic screen. Some of the thirty-three BGC products had been previously detected by UPLC-MS, like actinomycin D and deferoxamine B. Other BGCs had 0% homology to known BGCs, including a terpene BGC which only showed core gene homology to two other Streptomyces. One of these strains shared all of the BGCs with S. costaricanus, including their sequential order and closely approximated genomic locations. Comparison of marker genes with autoMLST gave preliminary evidence for the taxonomic reclassification of S. costaricanus as a strain of S. griseofuscus. Starting from a large collection of unexploited Streptomyces, this project catalogued the metabolomic and genomic diversity of a single strain and its bioactive potential. Together, the project stages formed a workflow for further exploitation of NCIMB Streptomyces and other microbes

J Am Chem Soc

Viridicatumtoxin (1) is a tetracycline-like fungal meroterpenoid with a unique, fused spirobicyclic ring system. Puzzlingly, no dedicated terpene cyclase is found in the gene cluster identified in Penicillium aethiopicum. Cytochrome P450 enzymes VrtE and VrtK in the vrt gene cluster were shown to catalyze C5-hydroxylation and spirobicyclic ring formation, respectively. Feeding acyclic previridicatumtoxin to Saccharomyces cerevisiae expressing VrtK confirmed that VrtK is the sole enzyme required for cyclizing the geranyl moiety. Thus, VrtK is the first example of a P450 that can catalyze terpene cyclization, most likely via initial oxidation of C17 to an allylic carbocation. Quantum chemical modeling revealed a possible new tertiary carbocation intermediate E that forms after allylic carbocation formation. Intermediate E can readily undergo concerted 1,2-alkyl shift/1,3-hydride shift, either spontaneously or further aided by VrtK, followed by C7 Friedel-Crafts alkylation to afford 1. The most likely stereochemical course of the reaction was proposed on the basis of the results of our computations.DP1 GM106413/GM/NIGMS NIH HHS/United States1R01GM085128/GM/NIGMS NIH HHS/United StatesGM-0846/GM/NIGMS NIH HHS/United StatesT32 GM008496/GM/NIGMS NIH HHS/United States1DP1GM106413/DP/NCCDPHP CDC HHS/United StatesR01 GM085128/GM/NIGMS NIH HHS/United States2014-11-13T00:00:00Z24161266PMC387205