PCR screening reveals considerable unexploited biosynthetic potential of ansamycins and a mysterious family of AHBA-containing natural products in actinomycetes

Double Bond Geometric Isomers of Pentaketide Ansamycins from Streptomyces sp. S008

Six new pentaketide ansamycins, namely, shengliangmycins A-F (1-6, respectively), were obtained from the fermentation products of Streptomyces sp. S008OEslmR2 that was derived by constitutive expression of LAL regulator gene slmR2. The structures of 1-6 were determined through comprehensive spectroscopic analysis and single-crystal X-ray diffraction. Compound 1 has a cis-C6═C7 bond, which is different from that of compounds 2-5. Compounds 3-6 feature a morpholinone structural moiety, whereas 5 is characterized by a pyrazoline ring, which is rare in natural products.

Combating Antimicrobial Resistance in the Post-Genomic Era: Rapid Antibiotic Discovery

Constantly evolving drug-resistant "superbugs" have caused an urgent demand for novel antimicrobial agents. Natural products and their analogs have been a prolific source of antimicrobial agents, even though a high rediscovery rate and less targeted research has made the field challenging in the pre-genomic era. With recent advancements in technology, natural product research is gaining new life. Genome mining has allowed for more targeted excavation of biosynthetic potential from natural sources that was previously overlooked. Researchers use bioinformatic algorithms to rapidly identify and predict antimicrobial candidates by studying the genome before even entering the lab. In addition, synthetic biology and advanced analytical instruments enable the accelerated identification of novel antibiotics with distinct structures. Here, we reviewed the literature for noteworthy examples of novel antimicrobial agents discovered through various methodologies, highlighting the candidates with potent effectiveness against antimicrobial-resistant pathogens.

Scalable Total Syntheses of (±)-Catellatolactams A and B

The first total syntheses of (±)-catellatolactams A and B, two novel ansamacrolactams, are described in 5 and 8 steps, respectively. The strategy relies on an amidation reaction to couple the acylated Meldrum's acid and an aryl amine, a regioselective C-H insertion to construct the γ-lactam moiety, and an RCM reaction to forge the macrocycles with E-olefin. This concise and scalable synthesis provided over 200 mg of the target molecules.

Arthrobacter wenxiniae sp. nov., a novel plant growth-promoting rhizobacteria species harbouring a carotenoids biosynthetic gene cluster

A bacterial strain, designated AETb3-4^T was isolated from the rhizosphere of lily. Comparison of 16S rRNA gene sequences showed that the sequence from strain AETb3-4^T exhibits high sequence similarity with those of Arthrobacter silviterrae KIS14-16^T (97.9%), Arthrobacter livingstonensis LI2^T (97.2%) and Arthrobacter stackebrandtii CCM 2783^T (97.0%). Whole genome average nucleotide identity (ANI) and the digital DNA-DNA hybridization (dDDH) values between strain AETb3-4T and the reference strains A. silviterrae DSM 27180^T, A. livingstonensis L12^T and A. stackebrandtii DSM 16005^T were below 83.6% and 27.7%, respectively, values which are considerably below the proposed thresholds for the species delineation, consistent with the proposal that strain AETb3-4^T represents a novel species. The genome size of strain AETb3-4^T is 4.33 Mb and the genomic DNA G + C content is 67.3%. The main polar lipids were identified as phosphatidylglycerol, diphosphatidylglycero, phosphatidylinositol and an unidentified glycolipid. The major fatty acids (> 10%) were identified as anteiso-C_{15: 0} and anteiso-C_{17: 0}. The predominant menaquinone was found to be menaquinone 9 (MK-9) (H₂) (82.2%). Phenotypic tests allowed the strain to be differentiated from its close phylogenetic neighbors. Based on the results obtained, it is proposed that the strain AETb3-4^T (= CFCC 16390^T = LMG 31708^T) represents a novel species in the genus Arthrobacter, for which the names Arthrobacter wenxiniae sp. nov. is proposed. In addition, the novel strain AETb3-4^T has multiple plant growth-promoting characters including ACC-deaminase activity and production of IAA. Furthermore, the genome contains secondary metabolite biosynthesis gene clusters, including a carotenoid biosynthetic gene cluster, suggesting potential capacities for secondary metabolite synthesis. These data suggest that strain AETb3-4^T may have potential applications both in medicine and sustainable agriculture.

Three new polyketides from vasR2 gene over-expressed mutant strain of Verrucosispora sp. NS0172

Over-expression of the pathway specific positive regulator gene is an effective way to activate silent gene cluster. In the curret study, the SARP family regulatory gene, vasR2, was over-expressed in strain Verrucosispora sp. NS0172 and the cryptic gene cluster responsible for the biosynthesis of pentaketide ansamycin was partially activated. Two tetraketides (1 and 2) and a triketide (3) ansamycins, together with five known compounds (4-8), were isolated and elucidated from strain NS0172OEvasR2. Their NMR data were completely assigned by analysis of their HR-ESI-MS and ¹H, ¹³C NMR, HMQC, HMBC and ¹H-¹H COSY spectra.

Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism

Rifamycin antibiotics (Rifs) target bacterial RNA polymerases (RNAPs) and are widely used to treat infections including tuberculosis. The utility of these compounds is threatened by the increasing incidence of resistance (RifR). As resistance mechanisms found in clinical settings may also occur in natural environments, here we postulated that bacteria could have evolved to produce rifamycin congeners active against clinically relevant resistance phenotypes. We survey soil metagenomes and identify a tailoring enzyme-rich family of gene clusters encoding biosynthesis of rifamycin congeners (kanglemycins, Kangs) with potent in vivo and in vitro activity against the most common clinically relevant RifR mutations. Our structural and mechanistic analyses reveal the basis for Kang inhibition of RifR RNAP. Unlike Rifs, Kangs function through a mechanism that includes interfering with 5'-initiating substrate binding. Our results suggest that examining soil microbiomes for new analogues of clinically used antibiotics may uncover metabolites capable of circumventing clinically important resistance mechanisms.

Complete Genome of Micromonospora sp. Strain B006 Reveals Biosynthetic Potential of a Lake Michigan Actinomycete

Actinomycete bacteria isolated from freshwater environments are an unexplored source of natural products. Here we report the complete genome of the Great Lakes-derived Micromonospora sp. strain B006, revealing its potential for natural product biosynthesis. The 7-megabase pair chromosome of strain B006 was sequenced using Illumina and Oxford Nanopore technologies followed by Sanger sequencing to close remaining gaps. All identified biosynthetic gene clusters (BGCs) were manually curated. Five known BGCs were identified encoding desferrioxamine, alkyl- O-dihydrogeranylmethoxyhydroquinone, a spore pigment, sioxanthin, and diazepinomicin, which is currently in phase II clinical trials to treat Phelan-McDermid syndrome and co-morbid epilepsy. We report here that strain B006 is indeed a producer of diazepinomicin and at yields higher than previously reported. Moreover, 11 of the 16 identified BGCs are orphan, eight of which were transcriptionally active under the culture condition tested. Orphan BGCs include an enediyne polyketide synthase and an uncharacteristically large, 36-module polyketide synthase-nonribosomal peptide synthetase BGC. We developed a genetics system for Micromonospora sp. B006 that will contribute to deorphaning BGCs in the future. This study is one of the few attempts to report the biosynthetic capacity of a freshwater-derived actinomycete and highlights this resource as a potential reservoir for new natural products.

Bioactivity Assessment of Indian Origin-Mangrove Actinobacteria against Candida albicans

Actinobacteria is found to have a potent metabolic activity against pathogens. The present study reveals the assessment of potent antifungal secondary metabolites from actinobacteria isolated from Indian marine mangrove sediments. The samples were collected from the coastal regions of Muthupet, Andaman and the Nicobar Islands. Identification was carried out using 16S rRNA analysis and biosynthetic genes (Polyketide synthase type I/II and Non-ribosomal peptide synthase) were screened. Actinobacteria were assayed for their antifungal activity against 16 clinical Candida albicans and the compound analysis was performed using gas chromatography-mass spectrometry GC-MS. The 31 actinobacterial strains were isolated and 16S rRNA gene sequencing revealed that this ecosystem is rich on actinobacteria, with Streptomyces as the predominant genus. The PCR based screening of biosynthetic genes revealed the presence of PKS-I in six strains, PKS-II in four strains and NRPS in 11 strains. The isolated actinobacteria VITGAP240 and VITGAP241 (two isolates) were found to have a potential antifungal activity against all the tested C. albicans. GC-MS results revealed that the actinobacterial compounds were belonging to heterocyclic, polyketides and peptides. Overall, the strains possess a wide spectrum of antifungal properties which affords the production of significant bioactive metabolites as potential antibiotics.

Pentaketide Ansamycin Microansamycins A-I from Micromonospora sp. Reveal Diverse Post-PKS Modifications

Overexpression of the pathway-specific positive regulator gene mas13 activated the cryptic gene cluster mas, resulting in the isolation of nine novel pentaketide ansamycins, namely, microansamycins A-I (1-9). These results not only revealed a biosynthetic gene cluster of pentaketide ansamycins for the first time but also presented an unprecedented scenario of diverse post-PKS modifications in ansamycin biosynthesis.

Phylogeny-guided (meta)genome mining approach for the targeted discovery of new microbial natural products

Genomics-based methods are now commonplace in natural products research. A phylogeny-guided mining approach provides a means to quickly screen a large number of microbial genomes or metagenomes in search of new biosynthetic gene clusters of interest. In this approach, biosynthetic genes serve as molecular markers, and phylogenetic trees built with known and unknown marker gene sequences are used to quickly prioritize biosynthetic gene clusters for their metabolites characterization. An increase in the use of this approach has been observed for the last couple of years along with the emergence of low cost sequencing technologies. The aim of this review is to discuss the basic concept of a phylogeny-guided mining approach, and also to provide examples in which this approach was successfully applied to discover new natural products from microbial genomes and metagenomes. I believe that the phylogeny-guided mining approach will continue to play an important role in genomics-based natural products research.

Ansavaricins A–E: five new streptovaricin derivatives from Streptomyces sp. S012

Five new polyketides of the ansamycin class, named ansavaricins A–E (1–5), together with three known streptovaricins 6–8, were isolated from the Streptomyces sp. S012 strain.

Ansavaricins F–I, new DNA topoisomerase inhibitors produced by Streptomyces sp. S012

Ansamycins are a family of macrolactams characterized by an aromatic chromophore with an aliphatic chain (ansa chain) connected back to a nonadjacent position through an amide bond.

Neoansamycins from Streptomyces sp. LZ35

Neoansamycins D–I with unusual extender units and diverse post-PKS modifications were isolated from the Streptomyces sp. SR201nam1OE strain.

D-Alanylation in the Assembly of Ansatrienin Side Chain Is Catalyzed by a Modular NRPS

Ansatrienins are a group of ansamycins with an N-cyclohexanoyl d-alanyl side chain. Though ansatrienins have been identified for decades, the mechanism for the addition of this unique side chain was not established. Here, we report the biochemical characterization of a tridomain nonribosomal peptide synthetase (NRPS), AstC, and an N-acyltransferase, AstF1, encoded in the biosynthetic pathway of ansatrienins. We demonstrate that AstC can efficiently catalyze the transfer of d-alanine to the C-11 hydroxyl group of ansatrienins, and AstF1 is able to attach the cyclohexanoyl group to the amino group of d-alanine. Remarkably, AstC presents the first example that a modular NRPS can catalyze intermolecular d-alanylation of the hydroxyl group to form an ester bond, though alanyl natural products have been known for decades. In addition, both AstC and AstF1 have broad substrate specificity toward acyl donors, which can be utilized to create novel ansatrienins.

Deletion of the side chain assembly reveals diverse post-PKS modifications in the biosynthesis of ansatrienins

Seven new ansatrienols were extracted from Streptomyces sp., and 3 showed anti-T3SS activity, demonstrating diverse post-PKS modifications during ansatrienin biosynthesis.

Activating a Cryptic Ansamycin Biosynthetic Gene Cluster To Produce Three New Naphthalenic Octaketide Ansamycins with n-Pentyl and n-Butyl Side Chains

Genome mining is a rational approach to discovering new natural products. The genome sequence analysis of Streptomyces sp. LZ35 revealed the presence of a putative ansamycin gene cluster (nam). Constitutive overexpression of the pathway-specific transcriptional regulatory gene nam1 successfully activated the nam gene cluster, and three novel naphthalenic octaketide ansamycins were discovered with unprecedented n-pentylmalonyl-CoA or n-butylmalonyl-CoA extender units. This study represents the first example of discovering novel ansamycin scaffolds via activation of a cryptic gene cluster.

Identification of AstG1, A LAL family regulator that positively controls ansatrienins production in Streptomyces sp. XZQH13

Ansamycins is a group of type I polyketides characterized by the unique starter unit 3-amino-5-hydroxybenzoic acid. This family of secondary metabolites shows diverse biological activities, well-known members of which include rifamycin, geldanamycin, and maytansine. Previously, we isolated an AHBA synthase gene-positive strain Streptomyces sp. XZQH13 containing a "silent" ansamycin biosynthetic gene cluster ast. The constitutive expression of the Large-ATP-binding regulators of the LuxR family regulator gene astG1 located within the cluster triggered the expression of the biosynthetic genes. Reverse transcription-PCR experiments showed that the expression of the key biosynthetic genes, astB4, astD1, and astF1, was induced in the astG1 overexpression mutant compared to the wild type. This led to the isolation of two known ansatrienins, hydroxymycotrienin A (1) and thiazinotrienomycin G (2), which were identified by analysis of the mass spectral and NMR spectral data, from the mutant. These observations suggest that astG1 is probably a pathway-specific positive regulator for the biosynthesis of ansatrienin.

Heterologous expression of galbonolide biosynthetic genes in Streptomyces coelicolor

The galbonolide antibiotics are non-glycosylated heptaketide 14-membered macrolides. These antibiotics exhibit broad-spectrum fungicidal activities, including against the human pathogen Cryptococcus neoformans. Previously, galbonolides B and E were isolated from the marine actinomycete Streptomyces sp. LZ35. By bioinformatics analysis, the putative galbonolide biosynthetic gene cluster, gbn, was identified in the genome of strain LZ35. In order to verify that the core genes (gbnA-E) are sufficient for synthesizing the basic structure of galbonolide as previously proposed, we performed the heterologous expression of gbnA-E in a "clean background" host Streptomyces coelicolor ZM12, in which all the native polyketide synthase genes have been deleted. As expected, the production of galbonolide B (1) was detected in the transformant. To the best of our knowledge, this is the first report that demonstrates the essential role of gbnA-E in the biosynthesis of galbonolides by heterologous expression. This heterologous expression system would be helpful to generate novel galbonolide derivatives by co-overexpression of unusual biosynthesis extender units.

Overexpression of div8 increases the production and diversity of divergolides in Streptomyces sp. W112

Isolation and structure elucidation of divergolides from Streptomyces sp. HKI0576 revealed unusual ansamycin diversification reactions and the biosynthetic flexibility of the divergolide family.

Endophytes are hidden producers of maytansine in Putterlickia roots

Several recent studies have lent evidence to the fact that certain so-called plant metabolites are actually biosynthesized by associated microorganisms. In this work, we show that the original source organism(s) responsible for the biosynthesis of the important anticancer and cytotoxic compound maytansine is the endophytic bacterial community harbored specifically within the roots of Putterlickia verrucosa and P. retrospinosa plants. Evaluation of the root endophytic community by chemical characterization of their fermentation products using HPLC-HRMS(n), along with a selective microbiological assay using the maytansine-sensitive type strain Hamigera avellanea revealed the endophytic production of maytansine. This was further confirmed by the presence of AHBA synthase genes in the root endophytic communities. Finally, MALDI-imaging-HRMS was used to demonstrate that maytansine produced by the endophytes is typically accumulated mainly in the root cortex of both plants. Our study, thus, reveals that maytansine is actually a biosynthetic product of root-associated endophytic microorganisms. The knowledge gained from this study provides fundamental insights on the biosynthesis of so-called plant metabolites by endophytes residing in distinct ecological niches.

Biosynthesis of hygrocins, antitumor naphthoquinone ansamycins produced by Streptomyces sp. LZ35

Hygrocins are naphthoquinone ansamycins with significant antitumor activities. Here, we report the identification and characterization of the hygrocin biosynthetic gene cluster (hgc) in Streptomyces sp. LZ35. A biosynthetic pathway is proposed based on bioinformatics analysis of the hgc genes and intermediates accumulated in selected gene disruption mutants. One of the steps during the biosynthesis of hygrocins is a Baeyer–Villiger oxidation between C5 and C6, catalyzed by luciferase- like monooxygenase homologue Hgc3. Hgc3 represents the founding member of a previously uncharacterized family of enzymes acting as Baeyer–Villiger monooxygenases.

Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds

Marine microorganisms continue to be a source of structurally and biologically novel compounds with potential use in the biotechnology industry. The unique physiochemical properties of the marine environment (such as pH, pressure, temperature, osmolarity) and uncommon functional groups (such as isonitrile, dichloroimine, isocyanate, and halogenated functional groups) are frequently found in marine metabolites. These facts have resulted in the production of bioactive substances with different properties than those found in terrestrial habitats. In fact, the marine environment contains a relatively untapped reservoir of bioactivity. Recent advances in genomics, metagenomics, proteomics, combinatorial biosynthesis, synthetic biology, screening methods, expression systems, bioinformatics, and the ever increasing availability of sequenced genomes provides us with more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts. The combination of these advanced techniques with traditional techniques, together with the use of dereplication strategies to eliminate known compounds, provides a powerful tool in the discovery of novel marine bioactive compounds. This review outlines and discusses the emerging strategies for the biodiscovery of these bioactive compounds.