scholarly journals Expanded Natural Product Diversity Revealed by Analysis of Lanthipeptide-Like Gene Clusters in Actinobacteria

2015 ◽  
Vol 81 (13) ◽  
pp. 4339-4350 ◽  
Author(s):  
Qi Zhang ◽  
James R. Doroghazi ◽  
Xiling Zhao ◽  
Mark C. Walker ◽  
Wilfred A. van der Donk
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Gene Cluster ◽  
Posttranslational Modifications ◽  
Large Scale ◽  
Biological Activities ◽  
Gene Clusters ◽  
Chemical Diversity ◽  
Content Type ◽  
Modified Peptides

ABSTRACTLanthionine-containing peptides (lanthipeptides) are a rapidly growing family of polycyclic peptide natural products belonging to the large class of ribosomally synthesized and posttranslationally modified peptides (RiPPs). Lanthipeptides are widely distributed in taxonomically distant species, and their currently known biosynthetic systems and biological activities are diverse. Building on the recent natural product gene cluster family (GCF) project, we report here large-scale analysis of lanthipeptide-like biosynthetic gene clusters fromActinobacteria. Our analysis suggests that lanthipeptide biosynthetic pathways, and by extrapolation the natural products themselves, are much more diverse than currently appreciated and contain many different posttranslational modifications. Furthermore, lanthionine synthetases are much more diverse in sequence and domain topology than currently characterized systems, and they are used by the biosynthetic machineries for natural products other than lanthipeptides. The gene cluster families described here significantly expand the chemical diversity and biosynthetic repertoire of lanthionine-related natural products. Biosynthesis of these novel natural products likely involves unusual and unprecedented biochemistries, as illustrated by several examples discussed in this study. In addition, class IV lanthipeptide gene clusters are shown not to be silent, setting the stage to investigate their biological activities.

scholarly journals Making drugs out of sunlight and ‘thin air’: an emerging synergy of synthetic biology and natural product chemistry

2020 ◽  
Vol 42 (4) ◽  
pp. 34-39
Author(s):  
Michael J. Stephenson ◽  
Anne Osbourn
Keyword(s):  
Natural Products ◽  
Synthetic Biology ◽  
Natural Product ◽  
Large Scale ◽  
Production Systems ◽  
Biological Activities ◽  
Structural Complexity ◽  
Scale Production ◽  
Natural Product Chemistry ◽  
Product Chemistry

Nature has long served as a rich source of structurally diverse small organic molecules with medicinally relevant biological activities. Despite the historical success of these so-called natural products, the enthusiasm of big pharma to explore these compounds as leads in drug design has waxed and waned. A major contributor to this is their often inherent structural complexity. Such compounds are difficult (often impossible) to access synthetically, a hurdle that can stifle lead development and hinder sustainable large-scale production of promising leads for clinical evaluation. However, in recent years, an emerging synergy between synthetic biology and natural product chemistry offers the potential for a renaissance in our ability to access natural products for drug discovery and development. Advances in genome sequencing, bioinformatics and the maturing of heterologous expression platforms are increasing, enabling the study, and ultimately, the manipulation of plant biosynthetic pathways. The triterpenes are one of the most structurally diverse families of natural products and arguably one of the most underrepresented in the clinic. The plant kingdom is the richest source of triterpene diversity, with >20,000 triterpenes reported so far. Transient expression of genes for candidate enzymes and pathways in amenable plant species is emerging as a powerful and rapid means of investigating and harnessing the plant enzymes involved in generating this diversity. Such platforms also have the potential to serve as production systems in their own right, with the possibility of upscaling these discoveries into commercially useful products using the same overall basic procedure. Ultimately, the carbon source for generation of high-value compounds in plants is photosynthesis. Therefore, we could, with the help of plants, be producing new medicines out of sunlight and ‘thin air’ in green factories in the not too distant future.

scholarly journals Evolution of Chemical Diversity in Echinocandin Lipopeptide Antifungal Metabolites

2015 ◽  
Vol 14 (7) ◽  
pp. 698-718 ◽  
Author(s):  
Qun Yue ◽  
Li Chen ◽  
Xiaoling Zhang ◽  
Kuan Li ◽  
Jingzu Sun ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Incomplete Lineage Sorting ◽  
Gene Clusters ◽  
Antifungal Drugs ◽  
Chemical Diversity ◽  
Specific Gene ◽  
Gene Trees ◽  
Content Type ◽  
Antifungal Metabolites ◽  
Pathway Gene

ABSTRACTThe echinocandins are a class of antifungal drugs that includes caspofungin, micafungin, and anidulafungin. Gene clusters encoding most of the structural complexity of the echinocandins provided a framework for hypotheses about the evolutionary history and chemical logic of echinocandin biosynthesis. Gene orthologs among echinocandin-producing fungi were identified. Pathway genes, including the nonribosomal peptide synthetases (NRPSs), were analyzed phylogenetically to address the hypothesis that these pathways represent descent from a common ancestor. The clusters share cooperative gene contents and linkages among the different strains. Individual pathway genes analyzed in the context of similar genes formed unique echinocandin-exclusive phylogenetic lineages. The echinocandin NRPSs, along with the NRPS from theinpgene cluster inAspergillus nidulansand its orthologs, comprise a novel lineage among fungal NRPSs. NRPS adenylation domains from different species exhibited a one-to-one correspondence between modules and amino acid specificity that is consistent with models of tandem duplication and subfunctionalization. Pathway gene trees and Ascomycota phylogenies are congruent and consistent with the hypothesis that the echinocandin gene clusters have a common origin. The disjunct Eurotiomycete-Leotiomycete distribution appears to be consistent with a scenario of vertical descent accompanied by incomplete lineage sorting and loss of the clusters from most lineages of theAscomycota. We present evidence for a single evolutionary origin of the echinocandin family of gene clusters and a progression of structural diversification in two fungal classes that diverged approximately 290 to 390 million years ago. Lineage-specific gene cluster evolution driven by selection of new chemotypes contributed to diversification of the molecular functionalities.

scholarly journals Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining

2016 ◽  
Vol 113 (42) ◽  
pp. E6343-E6351 ◽  
Author(s):  
Michael A. Skinnider ◽  
Chad W. Johnston ◽  
Robyn E. Edgar ◽  
Chris A. Dejong ◽  
Nishanth J. Merwin ◽  
...  
Keyword(s):  
Natural Products ◽  
Genome Sequencing ◽  
Sequence Data ◽  
Chemical Space ◽  
Biological Activities ◽  
Global Analysis ◽  
Gene Clusters ◽  
Systematic Investigation ◽  
Chemical Structures ◽  
Modified Peptides

Microbial natural products are an evolved resource of bioactive small molecules, which form the foundation of many modern therapeutic regimes. Ribosomally synthesized and posttranslationally modified peptides (RiPPs) represent a class of natural products which have attracted extensive interest for their diverse chemical structures and potent biological activities. Genome sequencing has revealed that the vast majority of genetically encoded natural products remain unknown. Many bioinformatic resources have therefore been developed to predict the chemical structures of natural products, particularly nonribosomal peptides and polyketides, from sequence data. However, the diversity and complexity of RiPPs have challenged systematic investigation of RiPP diversity, and consequently the vast majority of genetically encoded RiPPs remain chemical “dark matter.” Here, we introduce an algorithm to catalog RiPP biosynthetic gene clusters and chart genetically encoded RiPP chemical space. A global analysis of 65,421 prokaryotic genomes revealed 30,261 RiPP clusters, encoding 2,231 unique products. We further leverage the structure predictions generated by our algorithm to facilitate the genome-guided discovery of a molecule from a rare family of RiPPs. Our results provide the systematic investigation of RiPP genetic and chemical space, revealing the widespread distribution of RiPP biosynthesis throughout the prokaryotic tree of life, and provide a platform for the targeted discovery of RiPPs based on genome sequencing.

scholarly journals Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides

PLoS Biology ◽  
2020 ◽  
Vol 18 (12) ◽  
pp. e3001026
Author(s):  
Alexander M. Kloosterman ◽  
Peter Cimermancic ◽  
Somayah S. Elsayed ◽  
Chao Du ◽  
Michalis Hadjithomas ◽  
...  
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Sequence Similarity ◽  
Genome Mining ◽  
Gene Clusters ◽  
Support Vector ◽  
Chemical Labeling ◽  
Product Families ◽  
Anticancer Properties ◽  
Modified Peptides

Microbial natural products constitute a wide variety of chemical compounds, many which can have antibiotic, antiviral, or anticancer properties that make them interesting for clinical purposes. Natural product classes include polyketides (PKs), nonribosomal peptides (NRPs), and ribosomally synthesized and post-translationally modified peptides (RiPPs). While variants of biosynthetic gene clusters (BGCs) for known classes of natural products are easy to identify in genome sequences, BGCs for new compound classes escape attention. In particular, evidence is accumulating that for RiPPs, subclasses known thus far may only represent the tip of an iceberg. Here, we present decRiPPter (Data-driven Exploratory Class-independent RiPP TrackER), a RiPP genome mining algorithm aimed at the discovery of novel RiPP classes. DecRiPPter combines a Support Vector Machine (SVM) that identifies candidate RiPP precursors with pan-genomic analyses to identify which of these are encoded within operon-like structures that are part of the accessory genome of a genus. Subsequently, it prioritizes such regions based on the presence of new enzymology and based on patterns of gene cluster and precursor peptide conservation across species. We then applied decRiPPter to mine 1,295 Streptomyces genomes, which led to the identification of 42 new candidate RiPP families that could not be found by existing programs. One of these was studied further and elucidated as a representative of a novel subfamily of lanthipeptides, which we designate class V. The 2D structure of the new RiPP, which we name pristinin A3 (1), was solved using nuclear magnetic resonance (NMR), tandem mass spectrometry (MS/MS) data, and chemical labeling. Two previously unidentified modifying enzymes are proposed to create the hallmark lanthionine bridges. Taken together, our work highlights how novel natural product families can be discovered by methods going beyond sequence similarity searches to integrate multiple pathway discovery criteria.

scholarly journals Yeast homologous recombination-based promoter engineering for the activation of silent natural product biosynthetic gene clusters

2015 ◽  
Vol 112 (29) ◽  
pp. 8953-8958 ◽  
Author(s):  
Daniel Montiel ◽  
Hahk-Soo Kang ◽  
Fang-Yuan Chang ◽  
Zachary Charlop-Powers ◽  
Sean F. Brady
Keyword(s):  
Homologous Recombination ◽  
Natural Product ◽  
Gene Cluster ◽  
Large Scale ◽  
Gene Clusters ◽  
Marker Genes ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Silent Gene ◽  
Promoter Engineering

Large-scale sequencing of prokaryotic (meta)genomic DNA suggests that most bacterial natural product gene clusters are not expressed under common laboratory culture conditions. Silent gene clusters represent a promising resource for natural product discovery and the development of a new generation of therapeutics. Unfortunately, the characterization of molecules encoded by these clusters is hampered owing to our inability to express these gene clusters in the laboratory. To address this bottleneck, we have developed a promoter-engineering platform to transcriptionally activate silent gene clusters in a model heterologous host. Our approach uses yeast homologous recombination, an auxotrophy complementation-based yeast selection system and sequence orthogonal promoter cassettes to exchange all native promoters in silent gene clusters with constitutively active promoters. As part of this platform, we constructed and validated a set of bidirectional promoter cassettes consisting of orthogonal promoter sequences, Streptomyces ribosome binding sites, and yeast selectable marker genes. Using these tools we demonstrate the ability to simultaneously insert multiple promoter cassettes into a gene cluster, thereby expediting the reengineering process. We apply this method to model active and silent gene clusters (rebeccamycin and tetarimycin) and to the silent, cryptic pseudogene-containing, environmental DNA-derived Lzr gene cluster. Complete promoter refactoring and targeted gene exchange in this “dead” cluster led to the discovery of potent indolotryptoline antiproliferative agents, lazarimides A and B. This potentially scalable and cost-effective promoter reengineering platform should streamline the discovery of natural products from silent natural product biosynthetic gene clusters.

scholarly journals Coupling Mass Spectral and Genomic Information to Improve Bacterial Natural Product Discovery Workflows

Marine Drugs ◽  
2021 ◽  
Vol 19 (3) ◽  
pp. 142 ◽  
Author(s):  
Max Crüsemann
Keyword(s):  
Mass Spectrometry ◽  
Natural Products ◽  
Natural Product ◽  
Large Scale ◽  
Genome Mining ◽  
Structural Diversity ◽  
Gene Clusters ◽  
Genomic Information ◽  
Mass Spectral ◽  
Natural Product Discovery

Bacterial natural products possess potent bioactivities and high structural diversity and are typically encoded in biosynthetic gene clusters. Traditional natural product discovery approaches rely on UV- and bioassay-guided fractionation and are limited in terms of dereplication. Recent advances in mass spectrometry, sequencing and bioinformatics have led to large-scale accumulation of genomic and mass spectral data that is increasingly used for signature-based or correlation-based mass spectrometry genome mining approaches that enable rapid linking of metabolomic and genomic information to accelerate and rationalize natural product discovery. In this mini-review, these approaches are presented, and discovery examples provided. Finally, future opportunities and challenges for paired omics-based natural products discovery workflows are discussed.

scholarly journals Structure elucidation and biosynthesis of fuscachelins, peptide siderophores from the moderate thermophileThermobifida fusca

2008 ◽  
Vol 105 (40) ◽  
pp. 15311-15316 ◽  
Author(s):  
Eric J. Dimise ◽  
Paul F. Widboom ◽  
Steven D. Bruner
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Gene Cluster ◽  
Structure Elucidation ◽  
Biochemical Characterization ◽  
Gene Clusters ◽  
Biologically Active ◽  
Biosynthetic Gene ◽  
Nonribosomal Peptide

Bacteria belonging to the order Actinomycetales have proven to be an important source of biologically active and often therapeutically useful natural products. The characterization of orphan biosynthetic gene clusters is an emerging and valuable approach to the discovery of novel small molecules. Analysis of the recently sequenced genome of the thermophilic actinomyceteThermobifida fuscarevealed an orphan nonribosomal peptide biosynthetic gene cluster coding for an unknown siderophore natural product.T. fuscais a model organism for the study of thermostable cellulases and is a major degrader of plant cell walls. Here, we report the isolation and structure elucidation of the fuscachelins, siderophore natural products produced byT. fusca. In addition, we report the purification and biochemical characterization of the termination module of the nonribosomal peptide synthetase. Biochemical analysis of adenylation domain specificity supports the assignment of this gene cluster as the producer of the fuscachelin siderophores. The proposed nonribosomal peptide biosynthetic pathway exhibits several atypical features, including a macrocyclizing thioesterase that produces a 10-membered cyclic depsipeptide and a nonlinear assembly line, resulting in the unique heterodimeric architecture of the siderophore natural product.

scholarly journals Comparative Genomics and Metabolomics in the Genus Nocardia

mSystems ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Daniel Männle ◽  
Shaun M. K. McKinnie ◽  
Shrikant S. Mantri ◽  
Katharina Steinke ◽  
Zeyin Lu ◽  
...  
Keyword(s):  
Natural Product ◽  
Gene Cluster ◽  
Gene Clusters ◽  
Chemical Diversity ◽  
Biosynthetic Gene ◽  
Compound Identification ◽  
Biosynthetic Gene Clusters ◽  
Metabolomics Data ◽  
Similarity Networks ◽  
Gene Similarity

ABSTRACT Using automated genome analysis tools, it is often unclear to what degree genetic variability in homologous biosynthetic pathways relates to structural variation. This hampers strain prioritization and compound identification and can lead to overinterpretation of chemical diversity. Here, we assessed the metabolic potential of Nocardia, an underinvestigated actinobacterial genus that is known to comprise opportunistic human pathogens. Our analysis revealed a plethora of putative biosynthetic gene clusters of various classes, including polyketide, nonribosomal peptide, and terpenoid pathways. Furthermore, we used the highly conserved biosynthetic pathway for nocobactin-like siderophores to investigate how gene cluster differences correlate to structural differences in the produced compounds. Sequence similarity networks generated by BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) showed the presence of several distinct gene cluster families. Metabolic profiling of selected Nocardia strains using liquid chromatography-mass spectrometry (LC-MS) metabolomics data, nuclear magnetic resonance (NMR) spectroscopy, and GNPS (Global Natural Product Social molecular networking) revealed that nocobactin-like biosynthetic gene cluster (BGC) families above a BiG-SCAPE threshold of 70% can be assigned to distinct structural types of nocobactin-like siderophores. IMPORTANCE Our work emphasizes that Nocardia represent a prolific source for natural products rivaling better-characterized genera such as Streptomyces or Amycolatopsis. Furthermore, we showed that large-scale analysis of biosynthetic gene clusters using similarity networks with high stringency allows the distinction and prediction of natural product structural variations. This will facilitate future genomics-driven drug discovery campaigns.

scholarly journals Evolution of chemical diversity by coordinated gene swaps in type II polyketide gene clusters

2015 ◽  
Vol 112 (45) ◽  
pp. 13952-13957 ◽  
Author(s):  
Maureen E. Hillenmeyer ◽  
Gergana A. Vandova ◽  
Erin E. Berlew ◽  
Louise K. Charkoudian
Keyword(s):  
Rational Design ◽  
Large Scale ◽  
Biological Activities ◽  
Structural Complexity ◽  
Gene Clusters ◽  
Lessons Learned ◽  
Chemical Diversity ◽  
Type Ii ◽  
Cellular Processes ◽  
Wide Scale

Natural product biosynthetic pathways generate molecules of enormous structural complexity and exquisitely tuned biological activities. Studies of natural products have led to the discovery of many pharmaceutical agents, particularly antibiotics. Attempts to harness the catalytic prowess of biosynthetic enzyme systems, for both compound discovery and engineering, have been limited by a poor understanding of the evolution of the underlying gene clusters. We developed an approach to study the evolution of biosynthetic genes on a cluster-wide scale, integrating pairwise gene coevolution information with large-scale phylogenetic analysis. We used this method to infer the evolution of type II polyketide gene clusters, tracing the path of evolution from the single ancestor to those gene clusters surviving today. We identified 10 key gene types in these clusters, most of which were swapped in from existing cellular processes and subsequently specialized. The ancestral type II polyketide gene cluster likely comprised a core set of five genes, a roster that expanded and contracted throughout evolution. A key C24 ancestor diversified into major classes of longer and shorter chain length systems, from which a C20 ancestor gave rise to the majority of characterized type II polyketide antibiotics. Our findings reveal that (i) type II polyketide structure is predictable from its gene roster, (ii) only certain gene combinations are compatible, and (iii) gene swaps were likely a key to evolution of chemical diversity. The lessons learned about how natural selection drives polyketide chemical innovation can be applied to the rational design and guided discovery of chemicals with desired structures and properties.

scholarly journals Mining of Cyanobacterial Genomes Indicates That Plasmids Are Involved in the Production of Natural Products

2020 ◽  
Author(s):  
Rafael Popin ◽  
Danillo Alvarenga ◽  
Raquel Castelo-Branco ◽  
David Fewer ◽  
Kaarina Sivonen
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Biological Activities ◽  
Gene Clusters ◽  
Biosynthetic Pathways ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Chemical Structures ◽  
Wide Range ◽  
Genes Encoding

Abstract Background Microbial natural products have unique chemical structures and diverse biological activities. Cyanobacteria commonly possess a wide range of biosynthetic gene clusters to produce natural products. Several studies have mapped the distribution of natural product biosynthetic gene clusters in cyanobacterial genomes. However, little attention has been paid to natural product biosynthesis in plasmids. Some genes encoding cyanobacterial natural product biosynthetic pathways are believed to be dispersed by plasmids through horizontal gene transfer. Thus, we examined complete cyanobacterial genomes to assess if plasmids are involved in the production and dissemination of natural products by cyanobacteria.Results The 185 analyzed genomes possessed 1 to 42 gene clusters and an average of 10. In total, 1816 biosynthetic gene clusters were found. Approximately 95% of these clusters were present in chromosomes. The remaining 5% were present in plasmids, from which homologs of the biosynthetic pathways for aeruginosin, anabaenopeptin, ambiguine, cryptophycin, hassallidin, geosmin, and microcystin were manually curated. The cryptophycin pathway was previously described as active while the other gene cluster include all genes for biosynthesis. Approximately 12% of the 424 analyzed cyanobacterial plasmids contained homologs of genes involved in conjugation. Large plasmids, previously named as “chromids”, were also observed to be widespread in cyanobacteria. Sixteen cryptic natural product biosynthetic gene clusters and geosmin biosynthetic gene clusters were located in those mobile plasmids.Conclusion Homologues of genes involved in the production of toxins, protease inhibitors, odorous compounds, antimicrobials, antitumorals, and other unidentified natural products are located in cyanobacterial plasmids. Some of these plasmids are predicted to be conjugative. The present study provides in silico evidence that plasmids are involved in the distribution of natural product biosynthetic pathways in cyanobacteria.

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