scholarly journals In Situ Activation and Heterologous Production of a Cryptic Lantibiotic from an African Plant Ant-Derived Saccharopolyspora Species

2019 ◽  
Vol 86 (3) ◽  
Author(s):  
Eleni Vikeli ◽  
David A. Widdick ◽  
Sibyl F. D. Batey ◽  
Daniel Heine ◽  
Neil A. Holmes ◽  
...  
Keyword(s):  
Natural Products ◽  
Heterologous Expression ◽  
Gene Cluster ◽  
Ectopic Expression ◽  
Chemical Diversity ◽  
Ecological Niches ◽  
Heterologous Production ◽  
Biosynthetic Gene ◽  
Content Type ◽  
In Situ Activation

ABSTRACT Most clinical antibiotics are derived from actinomycete natural products discovered at least 60 years ago. However, the repeated rediscovery of known compounds led the pharmaceutical industry to largely discard microbial natural products (NPs) as a source of new chemical diversity. Recent advances in genome sequencing have revealed that these organisms have the potential to make many more NPs than previously thought. Approaches to unlock NP biosynthesis by genetic manipulation of strains, by the application of chemical genetics, or by microbial cocultivation have resulted in the identification of new antibacterial compounds. Concomitantly, intensive exploration of coevolved ecological niches, such as insect-microbe defensive symbioses, has revealed these to be a rich source of chemical novelty. Here, we report the new lanthipeptide antibiotic kyamicin, which was generated through the activation of a cryptic biosynthetic gene cluster identified by genome mining Saccharopolyspora species found in the obligate domatium-dwelling ant Tetraponera penzigi of the ant plant Vachellia drepanolobium. Transcriptional activation of this silent gene cluster was achieved by ectopic expression of a pathway-specific activator under the control of a constitutive promoter. Subsequently, a heterologous production platform was developed which enabled the purification of kyamicin for structural characterization and bioactivity determination. This strategy was also successful for the production of lantibiotics from other genera, paving the way for a synthetic heterologous expression platform for the discovery of lanthipeptides that are not detected under laboratory conditions or that are new to nature. IMPORTANCE The discovery of novel antibiotics to tackle the growing threat of antimicrobial resistance is impeded by difficulties in accessing the full biosynthetic potential of microorganisms. The development of new tools to unlock the biosynthesis of cryptic bacterial natural products will greatly increase the repertoire of natural product scaffolds. Here, we report a strategy for the ectopic expression of pathway-specific positive regulators that can be rapidly applied to activate the biosynthesis of cryptic lanthipeptide biosynthetic gene clusters. This allowed the discovery of a new lanthipeptide antibiotic directly from the native host and via heterologous expression.

scholarly journals In situ activation and heterologous production of a cryptic lantibiotic from a plant-ant derived Saccharopolyspora species

2019 ◽  
Author(s):  
Eleni Vikeli ◽  
David A. Widdick ◽  
Sibyl F. Batey ◽  
Daniel Heine ◽  
Neil A. Holmes ◽  
...  
Keyword(s):  
Natural Products ◽  
Heterologous Expression ◽  
Genetic Manipulation ◽  
Gene Clusters ◽  
Chemical Diversity ◽  
Ecological Niches ◽  
Heterologous Production ◽  
Biosynthetic Gene ◽  
Structural Characterisation ◽  
In Situ Activation

AbstractMost clinical antibiotics are derived from actinomycete natural products (NPs) discovered at least 60 years ago. Repeated rediscovery of known compounds led the pharmaceutical industry to largely discard microbial NPs as a source of new chemical diversity but advances in genome sequencing revealed that these organisms have the potential to make many more NPs than previously thought. Approaches to unlock NP biosynthesis by genetic manipulation of the strain, by the application of chemical genetics, or by microbial co-cultivation have resulted in the identification of new antibacterial compounds. Concomitantly, intensive exploration of coevolved ecological niches, such as insect-microbe defensive symbioses, has revealed these to be a rich source of chemical novelty. Here we report the novel lanthipeptide antibiotic kyamicin generated through the activation of a cryptic biosynthetic gene cluster identified by genome mining Saccharopolyspora species found in the obligate domatia-dwelling ant Tetraponera penzigi of the ant plant Vachellia drepanolobium. Heterologous production and purification of kyamicin allowed its structural characterisation and bioactivity determination. Our activation strategy was also successful for the expression of lantibiotics from other genera, paving the way for a synthetic heterologous expression platform for the discovery of lanthipeptides that are not detected under laboratory conditions or that are new to nature.ImportanceThe discovery of novel antibiotics to tackle the growing threat of antimicrobial resistance is impeded by difficulties in accessing the full biosynthetic potential of microorganisms. The development of new tools to unlock the biosynthesis of cryptic bacterial natural products will greatly increase the repertoire of natural product scaffolds. Here we report an activation strategy that can be rapidly applied to activate the biosynthesis of cryptic lanthipeptide biosynthetic gene clusters. This allowed the discovery of a new lanthipeptide antibiotic directly from the native host and via heterologous expression.

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 Heterologous Production of Cyanobacterial Mycosporine-Like Amino Acids Mycosporine-Ornithine and Mycosporine-Lysine in Escherichia coli

2016 ◽  
Vol 82 (20) ◽  
pp. 6167-6173 ◽  
Author(s):  
Meenu Katoch ◽  
Rabia Mazmouz ◽  
Rocky Chau ◽  
Leanne A. Pearson ◽  
Russell Pickford ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Heterologous Expression ◽  
Gene Cluster ◽  
Uv Radiation ◽  
Active Ingredient ◽  
Stress Factors ◽  
Heterologous Production ◽  
Content Type ◽  
E Coli

ABSTRACTMycosporine-like amino acids (MAAs) are an important class of secondary metabolites known for their protection against UV radiation and other stress factors. Cyanobacteria produce a variety of MAAs, including shinorine, the active ingredient in many sunscreen creams. Bioinformatic analysis of the genome of the soil-dwelling cyanobacteriumCylindrospermum stagnalePCC 7417 revealed a new gene cluster with homology to MAA synthase fromNostoc punctiforme. This newly identified gene cluster is unusual because it has five biosynthesis genes (mylAtomylE), compared to the four found in other MAA gene clusters. Heterologous expression ofmylAtomylEinEscherichia coliresulted in the production of mycosporine-lysine and the novel compound mycosporine-ornithine. To our knowledge, this is the first time these compounds have been heterologously produced inE. coliand structurally characterized via direct spectral guidance. This study offers insight into the diversity, biosynthesis, and structure of cyanobacterial MAAs and highlights their amenability to heterologous production methods.IMPORTANCEMycosporine-like amino acids (MAAs) are significant from an environmental microbiological perspective as they offer microbes protection against a variety of stress factors, including UV radiation. The heterologous expression of MAAs inE. coliis also significant from a biotechnological perspective as MAAs are the active ingredient in next-generation sunscreens.

scholarly journals The expansive library of jadomycins

2018 ◽  
Vol 96 (6) ◽  
pp. 495-501 ◽  
Author(s):  
Jeanna M. MacLeod ◽  
Stephanie M. Forget ◽  
David L. Jakeman
Keyword(s):  
Amino Acids ◽  
Natural Products ◽  
Amino Acid ◽  
Heterologous Expression ◽  
Gene Cluster ◽  
Gene Deletion ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Synthetic Derivatives ◽  
Subsequent Identification

The jadomycin family of natural products was discovered from Streptomyces venezuelae ISP5230 in the 1990s. Subsequent identification of the biosynthetic gene cluster along with synthetic efforts established that incorporation of an amino acid into the polyaromatic angucycline core occurs non-enzymatically. Over two decades, the precursor-directed biosynthetic potential of the jadomycins has been heavily exploited, generating a library exceeding 70 compounds. This review compiles the jadomycins that have been isolated and characterized to date; these include jadomycins incorporating proteinogenic and non-proteinogenic amino acids, semi-synthetic derivatives, biosynthetic shunt products, compounds isolated in structural gene deletion studies, and deoxysugar sugar variant jadomycins produced by deletion or heterologous expression of sugar biosynthetic genes.

Discovery and Heterologous Production of Sarubicins and Quinazolinone C-Glycosides with Protecting Activity for Cardiomyocytes

2021 ◽  
Author(s):  
Mingming Yu ◽  
Jianying Luo ◽  
Dan Luo ◽  
Qiang He ◽  
Yijun Yan ◽  
...  
Keyword(s):  
Natural Products ◽  
Gene Cluster ◽  
Genome Mining ◽  
Biosynthetic Gene Cluster ◽  
Heterologous Production ◽  
Biosynthetic Gene ◽  
Pharmaceutical Agents

Glycosylated natural products and their derivatives are important pharmaceutical agents. Genome mining of C-glycosylated metabolites biosynthetic gene cluster (BGC) from a soil-derived Streptomyces led to the isolation of sarubicins A...

scholarly journals Rhodococcus comparative genomics reveals a phylogenomic-dependent non-ribosomal peptide synthetase distribution: insights into biosynthetic gene cluster connection to an orphan metabolite

2021 ◽  
Vol 7 (7) ◽  
Author(s):  
Agustina Undabarrena ◽  
Ricardo Valencia ◽  
Andrés Cumsille ◽  
Leonardo Zamora-Leiva ◽  
Eduardo Castro-Nallar ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Gene Cluster ◽  
Sequence Similarity ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Chemical Diversity ◽  
Comparative Genomic ◽  
Biosynthetic Gene ◽  
Content Type ◽  
Link Type

Natural products (NPs) are synthesized by biosynthetic gene clusters (BGCs), whose genes are involved in producing one or a family of chemically related metabolites. Advances in comparative genomics have been favourable for exploiting huge amounts of data and discovering previously unknown BGCs. Nonetheless, studying distribution patterns of novel BGCs and elucidating the biosynthesis of orphan metabolites remains a challenge. To fill this knowledge gap, our study developed a pipeline for high-quality comparative genomics for the actinomycete genus Rhodococcus , which is metabolically versatile, yet understudied in terms of NPs, leading to a total of 110 genomes, 1891 BGCs and 717 non-ribosomal peptide synthetases (NRPSs). Phylogenomic inferences showed four major clades retrieved from strains of several ecological habitats. BiG-SCAPE sequence similarity BGC networking revealed 44 unidentified gene cluster families (GCFs) for NRPS, which presented a phylogenomic-dependent evolution pattern, supporting the hypothesis of vertical gene transfer. As a proof of concept, we analysed in-depth one of our marine strains, Rhodococcus sp. H-CA8f, which revealed a unique BGC distribution within its phylogenomic clade, involved in producing a chloramphenicol-related compound. While this BGC is part of the most abundant and widely distributed NRPS GCF, corason analysis unveiled major differences regarding its genetic context, co-occurrence patterns and modularity. This BGC is composed of three sections, two well-conserved right/left arms flanking a very variable middle section, composed of nrps genes. The presence of two non-canonical domains in H-CA8f’s BGC may contribute to adding chemical diversity to this family of NPs. Liquid chromatography-high resolution MS and dereplication efforts retrieved a set of related orphan metabolites, the corynecins, which to our knowledge are reported here for the first time in Rhodococcus . Overall, our data provide insights to connect BGC uniqueness with orphan metabolites, by revealing key comparative genomic features supported by models of BGC distribution along phylogeny.

scholarly journals Biosynthesis and Heterologous Expression of Cacaoidin, the First Member of the Lanthidin Family of RiPPs

Antibiotics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 403
Author(s):  
Fernando Román-Hurtado ◽  
Marina Sánchez-Hidalgo ◽  
Jesús Martín ◽  
Francisco Javier Ortiz-López ◽  
Olga Genilloud
Keyword(s):  
Heterologous Expression ◽  
Gene Cluster ◽  
Biosynthetic Gene Cluster ◽  
Heterologous Production ◽  
Biosynthetic Gene ◽  
Class V ◽  
First Report ◽  
Genome Databases ◽  
Complete Identification ◽  
Bioinformatic Tool

Cacaoidin is produced by the strain Streptomyces cacaoi CA-170360 and represents the first member of the new lanthidin (class V lanthipeptides) RiPP family. In this work, we describe the complete identification, cloning and heterologous expression of the cacaoidin biosynthetic gene cluster, which shows unique RiPP genes whose functions were not predicted by any bioinformatic tool. We also describe that the cacaoidin pathway is restricted to strains of the subspecies Streptomyces cacaoi subsp. cacaoi found in public genome databases, where we have also identified the presence of other putative class V lanthipeptide pathways. This is the first report on the heterologous production of a class V lanthipeptide.

Direct Cloning, Genetic Engineering, and Heterologous Expression of the Syringolin Biosynthetic Gene Cluster inE. colithrough Red/ET Recombineering

ChemBioChem ◽  
2012 ◽  
Vol 13 (13) ◽  
pp. 1946-1952 ◽  
Author(s):  
Xiaoying Bian ◽  
Fan Huang ◽  
Francis A. Stewart ◽  
Liqiu Xia ◽  
Youming Zhang ◽  
...  
Keyword(s):  
Genetic Engineering ◽  
Heterologous Expression ◽  
Gene Cluster ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Direct Cloning

Identification of the kinanthraquinone biosynthetic gene cluster by expression of an atypical response regulator

2021 ◽  
Vol 85 (3) ◽  
pp. 714-721
Author(s):  
Risa Takao ◽  
Katsuyuki Sakai ◽  
Hiroyuki Koshino ◽  
Hiroyuki Osada ◽  
Shunji Takahashi
Keyword(s):  
Heterologous Expression ◽  
Gene Cluster ◽  
Secondary Metabolite ◽  
Response Regulator ◽  
Bac Library ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Gene Organization ◽  
Biosynthetic Gene ◽  
Streptomyces Sp

ABSTRACT Recent advances in genome sequencing have revealed a variety of secondary metabolite biosynthetic gene clusters in actinomycetes. Understanding the biosynthetic mechanism controlling secondary metabolite production is important for utilizing these gene clusters. In this study, we focused on the kinanthraquinone biosynthetic gene cluster, which has not been identified yet in Streptomyces sp. SN-593. Based on chemical structure, 5 type II polyketide synthase gene clusters were listed from the genome sequence of Streptomyces sp. SN-593. Among them, a candidate gene cluster was selected by comparing the gene organization with grincamycin, which is synthesized through an intermediate similar to kinanthraquinone. We initially utilized a BAC library for subcloning the kiq gene cluster, performed heterologous expression in Streptomyces lividans TK23, and identified the production of kinanthraquinone and kinanthraquinone B. We also found that heterologous expression of kiqA, which belongs to the DNA-binding response regulator OmpR family, dramatically enhanced the production of kinanthraquinones.

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