Metagenomic domain substitution for the high-throughput modification of nonribosomal peptides.

The modular nature of nonribosomal peptide biosynthesis has driven efforts to generate peptide analogs by substituting amino acid-specifying domains within nonribosomal peptide synthetase (NRPS) enzymes. Rational NRPS engineering has increasingly focused on finding evolutionarily favored recombination sites for domain substitution. Here we present an alternative evolution-inspired approach that involves large-scale diversification and screening. By amplifying amino acid-specifying domains en masse from soil metagenomic DNA, we substitute more than 1,000 unique domains into a pyoverdine NRPS. Initial fluorescence and mass spectrometry screens followed by sequencing reveal more than 100 functional domain substitutions, collectively yielding 16 distinct pyoverdines as major products. This metagenomic approach does not require the high success rates demanded by rational NRPS engineering but instead enables the exploration of large numbers of substitutions in parallel. This opens possibilities for the discovery and production of nonribosomal peptides with diverse biological activities.

A metagenomic library cloning strategy that promotes high-level expression of captured genes to enable efficient functional screening.

Functional screening of environmental DNA (eDNA) libraries is a potentially powerful approach to discover enzymatic "unknown unknowns", but is usually heavily biased toward the tiny subset of genes preferentially transcribed and translated by the screening strain. We have overcome this by preparing an eDNA library via partial digest with restriction enzyme FatI (cuts CATG), causing a substantial proportion of ATG start codons to be precisely aligned with strong plasmid-encoded promoter and ribosome-binding sequences. Whereas we were unable to select nitroreductases from standard metagenome libraries, our FatI strategy yielded 21 nitroreductases spanning eight different enzyme families, each conferring resistance to the nitro-antibiotic niclosamide and sensitivity to the nitro-prodrug metronidazole. We showed expression could be improved by co-expressing rare tRNAs and encoded proteins purified directly using an embedded His6-tag. In a transgenic zebrafish model of metronidazole-mediated targeted cell ablation, our lead MhqN-family nitroreductase proved ∼5-fold more effective than the canonical nitroreductase NfsB.

Directed Evolution of the BpsA Carrier Protein Domain for Recognition by Non-cognate 4'-Phosphopantetheinyl Transferases to Enable Inhibitor Screening.

4'-Phosphopantetheinyl transferases (PPTases) play an essential role in activating the carrier protein domains of mega-synthases involved in primary and secondary metabolism and have been validated as promising drug targets in multiple pathogens. Monitoring phosphopantetheinylation of the non-ribosomal peptidase synthetase BpsA, which produces blue indigoidine pigment upon activation, is a useful strategy to screen chemical collections for inhibitors of a target PPTase. However, PPTases can exhibit carrier protein specificity and some medically important PPTases do not activate BpsA. Here, we describe how to conduct a directed evolution campaign to evolve the BpsA carrier protein domain for improved recognition by a candidate PPTase, as exemplified for the human Sfp-like PPTase. This method can be applied to other non-cognate PPTases for discovery of new drug candidates or chemical probes, or to enable development of next-generation biosensors that utilize BpsA as a reporter.

A metagenomic library cloning strategy that promotes high-level expression of captured genes to enable efficient functional screening.

Functional screening of environmental DNA (eDNA) libraries is a potentially powerful approach to discover enzymatic "unknown unknowns", but is usually heavily biased toward the tiny subset of genes preferentially transcribed and translated by the screening strain. We have overcome this by preparing an eDNA library via partial digest with restriction enzyme FatI (cuts CATG), causing a substantial proportion of ATG start codons to be precisely aligned with strong plasmid-encoded promoter and ribosome-binding sequences. Whereas we were unable to select nitroreductases from standard metagenome libraries, our FatI strategy yielded 21 nitroreductases spanning eight different enzyme families, each conferring resistance to the nitro-antibiotic niclosamide and sensitivity to the nitro-prodrug metronidazole. We showed expression could be improved by co-expressing rare tRNAs and encoded proteins purified directly using an embedded His6-tag. In a transgenic zebrafish model of metronidazole-mediated targeted cell ablation, our lead MhqN-family nitroreductase proved ~5-fold more effective than the canonical nitroreductase NfsB.

Stictamycin, an Aromatic Polyketide Antibiotic Isolated from a New Zealand Lichen-Sourced Streptomyces Species.

Here we describe the isolation and characterization of stictamycin, a new aromatic polyketide with activity against Staphylococcus aureus. Stictamycin was identified following metabolic profiling and bioactivity guided fractionation of organic extracts from Streptomyces sp. 438-3, an isolate from the New Zealand lichen Sticta felix. Comprehensive 1D and 2D NMR analyses were performed to determine the planar structure of stictamycin and relative configurations of stereo centers, with subsequent comparison of experimental and theoretical ECD spectra allowing elucidation of the absolute configuration. Whole-genome sequencing and biosynthetic gene cluster (BGC) analysis revealed that the Streptomyces sp. 438-3 strain contains an atypical type II polyketide (T2PKS) BGC capable of assembling polycyclic-aromatic ring skeletons. Cloning and knockout studies of this T2PKS BGC were used to confirm that it is responsible for the biosynthesis of stictamycin and elucidate a plausible biosynthetic scheme.

A Genomic Survey of the Natural Product Biosynthetic Potential of Actinomycetes Isolated from New Zealand Lichens.

Actinomycetes are prolific producers of industrially valuable and medically important compounds. Historically, the most efficient method of obtaining compounds has been bioactivity-guided isolation and characterization of drug-like molecules from culturable soil actinomycetes. Unfortunately, this pipeline has been met with an increasing number of rediscoveries, to the point where it is no longer considered an attractive approach for drug discovery. To address this challenge and to continue finding new compounds, researchers have increasingly focused on alternative environmental niches and screening methods. Here, we report the genetic investigation of actinomycetes from an underexplored source, New Zealand lichens. In this work, we obtain draft genome sequences for 322 lichen-associated actinomycetes. We then explore this genetic resource with an emphasis on biosynthetic potential. By enumerating biosynthetic gene clusters (BGCs) in our data sets and comparing these to various reference collections, we demonstrate that actinomycetes sourced from New Zealand lichens have the genetic capacity to produce large numbers of natural products, many of which are expected to be broadly different from those identified in previous efforts predominantly based on soil samples. Our data shed light on the actinomycete assemblage in New Zealand lichens and demonstrate that lichen-sourced actinobacteria could serve as reservoirs for discovering new secondary metabolites. IMPORTANCE Lichens are home to complex and distinctive microbial cohorts that have not been extensively explored for the ability to produce novel secondary metabolites. Here, we isolate and obtain genome sequence data for 322 actinomycetes from New Zealand lichens. In doing so, we delineate at least 85 potentially undescribed species, and show that lichen associated actinomycetes have the potential to yield many new secondary metabolites, and as such, might serve as a productive starting point for drug discovery efforts.

Draft Genome Sequence of a Novel Rhizobium Species Isolated from the Marine Macroalga Codium fragile (Oyster Thief).

In the process of studying the relationship between marine macroalgae and their bacterial symbionts, we isolated a new species of Rhizobium, which we designated Rhizobium sp. nov. C1 (for "Codium 1"). Here, we report the complete genome sequence of Rhizobium sp. nov. C1.

Preparation of Soil Metagenome Libraries and Screening for Gene-Specific Amplicons.

Cosmid libraries constructed from environmental metagenome samples are powerful tools for capturing the genomic diversity of complex microbial communities. The large insert size (∼35 kb) of such libraries means they are compatible with downstream expression of large biosynthetic gene clusters (BGCs). This allows the discovery of previously undescribed natural products that would be inaccessible using traditional culture-based discovery pipelines. Here we describe methods for the construction of a cosmid metagenome library from a soil sample, and the process of screening that library for individual cosmid clones containing aromatic polyketide BGCs using degenerate primers that target the ketosynthase alpha (KSα) gene.

Skyllamycins D and E, Non-Ribosomal Cyclic Depsipeptides from Lichen-Sourced Streptomyces anulatus.

The skyllamycins are a class of heavily modified, non-ribosomal peptides, first isolated from Streptomyces sp. KY11784. A Streptomyces strain with potent antibiotic activity against Bacillus subtilis was isolated from a sample of the New Zealand lichen Pseudocyphellaria dissimilis. Whole genome sequencing and biosynthetic gene cluster genetic analysis coupled with GNPS LCMS/MS molecular networking revealed that this strain had the capacity to produce skyllamycins, including previously undescribed congeners, and that these were likely the source of the observed biological activity. Guided by the results of the molecular networking, we isolated the previously reported skyllamycins A-C (1-3), along with two new congeners, skyllamycins D (4) and E (5). The structures of these compounds were elucidated using comprehensive 1D and 2D NMR analyses, along with HRESIMS fragmentation experiments. Antibacterial assays revealed that skyllamycin D possessed improved activity against B. subtilis E168 compared to previously reported congeners.

Metathramycin, a new bioactive aureolic acid discovered by heterologous expression of a metagenome derived biosynthetic pathway.

Bacterial natural products have been a rich source of bioactive compounds for drug development, and advances in DNA sequencing, informatics and molecular biology have opened new avenues for their discovery. Here, we describe the isolation of an aureolic acid biosynthetic gene cluster from a metagenome library derived from a New Zealand soil sample. Heterologous expression of this pathway in Streptomyces albus resulted in the production and isolation of two new aureolic acid compounds, one of which (metathramycin, 6) possesses potent bioactivity against a human colon carcinoma cell line (HCT-116, IC50 = 14.6 nM). As metathramycin was a minor constituent of the fermentation extract, its discovery relied on a combination of approaches including bioactivity guided fractionation, MS/MS characterisation and pathway engineering. This study not only demonstrates the presence of previously uncharacterised aureolic acids in the environment, but also the value of an integrated natural product discovery approach which may be generally applicable to low abundance bioactive metabolites.

Inhibition of Indigoidine Synthesis as a High-Throughput Colourimetric Screen for Antibiotics Targeting the Essential Mycobacterium tuberculosis Phosphopantetheinyl Transferase PptT.

A recently-validated and underexplored drug target in Mycobacterium tuberculosis is PptT, an essential phosphopantetheinyl transferase (PPTase) that plays a critical role in activating enzymes for both primary and secondary metabolism. PptT possesses a deep binding pocket that does not readily accept labelled coenzyme A analogues that have previously been used to screen for PPTase inhibitors. Here we report on the development of a high throughput, colourimetric screen that monitors the PptT-mediated activation of the non-ribosomal peptide synthetase BpsA to a blue pigment (indigoidine) synthesising form in vitro. This screen uses unadulterated coenzyme A, avoiding analogues that may interfere with inhibitor binding, and requires only a single-endpoint measurement. We benchmark the screen using the well-characterised Library of Pharmaceutically Active Compounds (LOPAC1280) collection and show that it is both sensitive and able to distinguish weak from strong inhibitors. We further show that the BpsA assay can be applied to quantify the level of inhibition and generate consistent EC50 data. We anticipate these tools will facilitate both the screening of established chemical collections to identify new anti-mycobacterial drug leads and to guide the exploration of structure-activity landscapes to improve existing PPTase inhibitors.

Complete Genome Sequence of a Novel Pseudomonas fluorescens Strain Isolated from the Flower of Kumarahou (Pomaderris kumeraho).

Kumarahou (Pomaderris kumeraho) is a shrub endemic to New Zealand used in rongoa (traditional medicine). While studying the antimicrobial properties of kumarahou, we isolated a new strain of Pseudomonas fluorescens, which we designated KF1 (for "kumarahou flower 1"). Here, we report the complete genome sequence of P. fluorescens KF1.

Hydrated Rubrolides from the New Zealand Tunicate Synoicum kuranui.

LCMS analysis of an extract of the New Zealand tunicate Synoicum kuranui showed evidence for numerous new rubrolides. Following a mass spectrometry-guided isolation procedure, new hydrated rubrolides V and W (5 and 6), along with previously reported rubrolide G (3), were isolated and characterized using MS and NMR. The anti-bacterial and cell cytotoxic activity of the compounds were compared to the potent anti-MRSA compound rubrolide A; hydration across the C-5/C-6 bond was shown to abrogate antibacterial activity.

Directed Evolution of the Nonribosomal Peptide Synthetase BpsA to Enable Recognition by the Human Phosphopantetheinyl Transferase for Counter-Screening Antibiotic Candidates.

Bacterial type II phosphopantetheinyl transferases (PPTases), required for the activation of many cellular mega-synthases, have been validated as promising drug targets in several pathogens. Activation of the blue-pigment-synthesizing nonribosomal peptide synthetase BpsA by a target PPTase can be used to screen in vitro for new antibiotic candidates from chemical libraries. For a complete screening platform, there is a need to also counter-screen inhibitors for cross-reactivity with the endogenous human Type II PPTase (hPPTase), as this is a likely source of toxicity. As hPPTase is unable to recognize the PCP-domain of native BpsA, we used a combination of directed evolution and rational engineering to generate a triple-substitution variant that is able to be efficiently activated by hPPTase. Our engineered BpsA variant was able to readily detect inhibition of both hPPTase and the equivalent rat PPTase by broad-spectrum PPTase inhibitors, demonstrating its potential for high-throughput counter-screening of novel antibiotic candidates.

Efficient rational modification of non-ribosomal peptides by adenylation domain substitution.

Non-ribosomal peptide synthetase (NRPS) enzymes form modular assembly-lines, wherein each module governs the incorporation of a specific monomer into a short peptide product. Modules are comprised of one or more key domains, including adenylation (A) domains, which recognise and activate the monomer substrate; condensation (C) domains, which catalyse amide bond formation; and thiolation (T) domains, which shuttle reaction intermediates between catalytic domains. This arrangement offers prospects for rational peptide modification via substitution of substrate-specifying domains. For over 20 years, it has been considered that C domains play key roles in proof-reading the substrate; a presumption that has greatly complicated rational NRPS redesign. Here we present evidence from both directed and natural evolution studies that any substrate-specifying role for C domains is likely to be the exception rather than the rule, and that novel non-ribosomal peptides can be generated by substitution of A domains alone. We identify permissive A domain recombination boundaries and show that these allow us to efficiently generate modified pyoverdine peptides at high yields. We further demonstrate the transferability of our approach in the PheATE-ProCAT model system originally used to infer C domain substrate specificity, generating modified dipeptide products at yields that are inconsistent with the prevailing dogma.

The indigoidine synthetase BpsA provides a colorimetric ATP assay that can be adapted to quantify the substrate preferences of other NRPS enzymes.

OBJECTIVES: To develop a colorimetric assay for ATP based on the blue-pigment synthesising non-ribosomal peptide synthetase (NRPS) BpsA, and to demonstrate its utility in defining the substrate specificity of other NRPS enzymes. RESULTS: BpsA is able to convert two molecules of L-glutamine into the readily-detected blue pigment indigoidine, consuming two molecules of ATP in the process. We showed that the stoichiometry of this reaction is robust and that it can be performed in a microplate format to accurately quantify ATP concentrations to low micromolar levels in a variety of media, using a spectrophotometric plate-reader. We also demonstrated that the assay can be adapted to evaluate the amino acid substrate preferences of NRPS adenylation domains, by adding pyrophosphatase enzyme to drive consumption of ATP in the presence of the preferred substrate. CONCLUSIONS: The robust nature and simplicity of the reaction protocol offers advantages over existing methods for ATP quantification and NRPS substrate analysis.

Targeted Isolation of Rubrolides from the New Zealand Marine Tunicate Synoicum kuranui.

Global natural products social (GNPS) molecular networking is a useful tool to categorize chemical space within samples and streamline the discovery of new natural products. Here, we demonstrate its use in chemically profiling the extract of the marine tunicate Synoicum kuranui, comprised of many previously reported rubrolides, for new chemical entities. Within the rubrolide cluster, two masses that did not correspond to previously reported congeners were detected, and, following MS-guided fractionation, led to the isolation of new methylated rubrolides T (3) and (Z/E)-U (4). Both compounds showed strong growth inhibitory activity against the Gram-positive bacteria Bacillus subtilis, with minimum inhibitory concentration (MIC) values of 0.41 and 0.91 µM, respectively.

Metagenomic Exploration of the Marine Sponge Mycale hentscheli Uncovers Multiple Polyketide-Producing Bacterial Symbionts.

Marine sponges have been a prolific source of unique bioactive compounds that are presumed to act as a deterrent to predation. Many of these compounds have potential therapeutic applications; however, the lack of efficient and sustainable synthetic routes frequently limits clinical development. Here, we describe a metagenomic investigation of Mycale hentscheli, a chemically gifted marine sponge that possesses multiple distinct chemotypes. We applied shotgun metagenomic sequencing, hybrid assembly of short- and long-read data, and metagenomic binning to obtain a comprehensive picture of the microbiome of five specimens, spanning three chemotypes. Our data revealed multiple producing species, each having relatively modest secondary metabolomes, that contribute collectively to the chemical arsenal of the holobiont. We assembled complete genomes for multiple new genera, including two species that produce the cytotoxic polyketides pateamine and mycalamide, as well as a third high-abundance symbiont harboring a proteusin-type biosynthetic pathway that appears to encode a new polytheonamide-like compound. We also identified an additional 188 biosynthetic gene clusters, including a pathway for biosynthesis of peloruside. These results suggest that multiple species cooperatively contribute to defensive symbiosis in M. hentscheli and reveal that the taxonomic diversity of secondary-metabolite-producing sponge symbionts is larger and richer than previously recognized.IMPORTANCEMycale hentscheli is a marine sponge that is rich in bioactive small molecules. Here, we use direct metagenomic sequencing to elucidate highly complete and contiguous genomes for the major symbiotic bacteria of this sponge. We identify complete biosynthetic pathways for the three potent cytotoxic polyketides which have previously been isolated from M. hentscheli Remarkably, and in contrast to previous studies of marine sponges, we attribute each of these metabolites to a different producing microbe. We also find that the microbiome of M. hentscheli is stably maintained among individuals, even over long periods of time. Collectively, our data suggest a cooperative mode of defensive symbiosis in which multiple symbiotic bacterial species cooperatively contribute to the defensive chemical arsenal of the holobiont.

Metagenome Driven Discovery of Nonribosomal Peptides.

Declining rates of novel natural product discovery and exponential rates of rediscovery heralded the end of the 1940s to 1960s "golden era" of antibiotic discovery. Fifty years later, the implementation of molecular screening methodologies revealed that standard culture-based screening approaches had failed to capture the vast majority of environmental bacteria and that even for the cultivable isolates only a small fraction of the biosynthetic potential had been tapped. A diversity of metagenomic screening and synthetic biology approaches have been developed to address these issues. The nonribosomal peptides have received particular focus, owing to their high levels of bioactivity and the predictability of the biosynthetic logic of the genetically encoded assembly lines that produce them. By uniting advances in next-generation sequencing and bioinformatic analysis with a diversity of traditional disciplines, several pioneering teams have proven that this previously inaccessible resource is no longer out of reach.

Uncovering the biosynthetic potential of rare metagenomic DNA using co-occurrence network analysis of targeted sequences.

Sequencing of DNA extracted from environmental samples can provide key insights into the biosynthetic potential of uncultured bacteria. However, the high complexity of soil metagenomes, which can contain thousands of bacterial species per gram of soil, imposes significant challenges to explore secondary metabolites potentially produced by rare members of the soil microbiome. Here, we develop a targeted sequencing workflow termed CONKAT-seq (co-occurrence network analysis of targeted sequences) that detects physically clustered biosynthetic domains, a hallmark of bacterial secondary metabolism. Following targeted amplification of conserved biosynthetic domains in a highly partitioned metagenomic library, CONKAT-seq evaluates amplicon co-occurrence patterns across library subpools to identify chromosomally clustered domains. We show that a single soil sample can contain more than a thousand uncharacterized biosynthetic gene clusters, most of which originate from low frequency genomes which are practically inaccessible through untargeted sequencing. CONKAT-seq allows scalable exploration of largely untapped biosynthetic diversity across multiple soils, and can guide the discovery of novel secondary metabolites from rare members of the soil microbiome.