Shipworm symbiosis ecology-guided discovery of an antibiotic that kills colistin-resistant Acinetobacter

2020 ◽  
Author(s):  
Bailey W. Miller ◽  
Albebson L. Lim ◽  
Zhenjian Lin ◽  
Jeannie Bailey ◽  
Louis R. Barrows ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Gene Clusters ◽  
Bacterial Symbiont ◽  
Health Needs ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Guided Discovery ◽  
Lipopeptide Antibiotics ◽  
Unmet Health Needs ◽  
The World

<i>Teredinibacter turnerae</i> is an intracellular bacterial symbiont that lives in the gills of wood-eating shipworms, where it is proposed to use antibiotics to defend itself and its animal host. Several biosynthetic gene clusters are conserved in <i>T. turnerae</i> and in their host shipworms around the world, implying that they encode the important defensive antibiotics. Here, we describe the turnercyclamycins, lipopeptide antibiotics encoded in the genomes of all sequenced T. turnerae strains. Turnercyclamycins A and B are bactericidal against challenging Gram-negative pathogens, including <i>Escherichia coli,</i> <i>Klebsiella pneumoniae</i>, and <i>Acinetobacter baumannii,</i> at 1, 2, and 8 µg/mL, respectively. Additionally, these compounds kill colistin-resistant <i>Acinetobacter </i>strains, while lacking toxicity to mammalian cells. Phenotypic screening identified the outer membrane as the likely target. By exploring the inhabitants of environments that select for the properties we require, we can harvest the fruits of evolution to discover compounds with potential to target unmet health needs. Investigating the symbionts of animals, and shipworms in particular, is a powerful example of this principle.

scholarly journals Shipworm symbiosis ecology-guided discovery of an antibiotic that kills colistin-resistant Acinetobacter

2020 ◽  
Author(s):  
Bailey W. Miller ◽  
Albebson L. Lim ◽  
Zhenjian Lin ◽  
Jeannie Bailey ◽  
Louis R. Barrows ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Gene Clusters ◽  
Bacterial Symbiont ◽  
Health Needs ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Guided Discovery ◽  
Lipopeptide Antibiotics ◽  
Unmet Health Needs ◽  
The World

<i>Teredinibacter turnerae</i> is an intracellular bacterial symbiont that lives in the gills of wood-eating shipworms, where it is proposed to use antibiotics to defend itself and its animal host. Several biosynthetic gene clusters are conserved in <i>T. turnerae</i> and in their host shipworms around the world, implying that they encode the important defensive antibiotics. Here, we describe the turnercyclamycins, lipopeptide antibiotics encoded in the genomes of all sequenced T. turnerae strains. Turnercyclamycins A and B are bactericidal against challenging Gram-negative pathogens, including <i>Escherichia coli,</i> <i>Klebsiella pneumoniae</i>, and <i>Acinetobacter baumannii,</i> at 1, 2, and 8 µg/mL, respectively. Additionally, these compounds kill colistin-resistant <i>Acinetobacter </i>strains, while lacking toxicity to mammalian cells. Phenotypic screening identified the outer membrane as the likely target. By exploring the inhabitants of environments that select for the properties we require, we can harvest the fruits of evolution to discover compounds with potential to target unmet health needs. Investigating the symbionts of animals, and shipworms in particular, is a powerful example of this principle.

Shipworm Symbiosis Ecology-Guided Discovery of Gram-Negative Selective Antibiotic with Activity Against Acinetobacter

2020 ◽  
Author(s):  
Bailey W. Miller ◽  
Albebson L. Lim ◽  
Zhenjian Lin ◽  
Jeannie Bailey ◽  
Louis R. Barrows ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Gene Clusters ◽  
Bacterial Symbiont ◽  
Health Needs ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Guided Discovery ◽  
Gram Negative ◽  
Lipopeptide Antibiotics ◽  
Unmet Health Needs

<i>Teredinibacter turnerae</i> is an intracellular bacterial symbiont that lives in the gills of wood-eating shipworms, where it is proposed to use antibiotics to defend itself and its animal host. Several biosynthetic gene clusters are conserved in <i>T. turnerae</i> and in their host shipworms around the world, implying that they encode the important defensive antibiotics. Here, we describe the turnercyclamycins, lipopeptide antibiotics encoded in the genomes of all sequenced T. turnerae strains. Turnercyclamycins A and B are bactericidal against challenging Gram-negative pathogens, <i>Escherichia coli,</i> <i>Klebsiella pneumoniae</i>, and <i>Acinetobacter baumannii,</i> at 1, 2, and 8 µg/mL, respectively, while lacking toxicity to mammalian cells. Phenotypic screening identified the outer membrane as the likely target. By exploring the inhabitants of environments that select for the properties we require, we can harvest the fruits of evolution to discover compounds with potential to target unmet health needs. Investigating the symbionts of animals, and shipworms in particular, is a powerful example of this principle.

scholarly journals Genome-Guided Discovery of Natural Products through Multiplexed Low-Coverage Whole-Genome Sequencing of Soil Actinomycetes on Oxford Nanopore Flongle

mSystems ◽  
2021 ◽  
Author(s):  
Rahim Rajwani ◽  
Shannon I. Ohlemacher ◽  
Gengxiang Zhao ◽  
Hong-Bing Liu ◽  
Carole A. Bewley
Keyword(s):  
Low Cost ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Guided Discovery ◽  
Short Read Sequencing ◽  
Oxford Nanopore ◽  
Soil Actinomycetes ◽  
Actinomycete Strain ◽  
Low Coverage

Short-read sequencing of GC-rich genomes such as those from actinomycetes results in a fragmented genome assembly and truncated biosynthetic gene clusters (often 10 to >100 kb long), which hinders our ability to understand the biosynthetic potential of a given strain and predict the molecules that can be produced. The current study demonstrates that contiguous DNA assemblies, suitable for analysis of BGCs, can be obtained through low-coverage, multiplexed sequencing on Flongle, which provides a new low-cost workflow ($30 to 40 per strain) for sequencing actinomycete strain libraries.

scholarly journals Discovery of recombinases enables genome mining of cryptic biosynthetic gene clusters in Burkholderiales species

2018 ◽  
Vol 115 (18) ◽  
pp. E4255-E4263 ◽  
Author(s):  
Xue Wang ◽  
Haibo Zhou ◽  
Hanna Chen ◽  
Xiaoshu Jing ◽  
Wentao Zheng ◽  
...  
Keyword(s):  
Genome Engineering ◽  
Polyketide Synthase ◽  
Genome Mining ◽  
Gene Clusters ◽  
Genetic System ◽  
Spectroscopic Characterization ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Guided Discovery ◽  
Genetic Tools

Bacterial genomes encode numerous cryptic biosynthetic gene clusters (BGCs) that represent a largely untapped source of drugs or pesticides. Mining of the cryptic products is limited by the unavailability of streamlined genetic tools in native producers. Precise genome engineering using bacteriophage recombinases is particularly useful for genome mining. However, recombinases are usually host-specific. The genome-guided discovery of novel recombinases and their transient expression could boost cryptic BGC mining. Herein, we reported a genetic system employing Red recombinases from Burkholderiales strain DSM 7029 for efficient genome engineering in several Burkholderiales species that currently lack effective genetic tools. Using specialized recombinases-assisted in situ insertion of functional promoters, we successfully mined five cryptic nonribosomal peptide synthetase/polyketide synthase BGCs, two of which were silent. Two classes of lipopeptides, glidopeptins and rhizomides, were identified through extensive spectroscopic characterization. This recombinase expression strategy offers utility within other bacteria species, allowing bioprospecting for potentially scalable discovery of novel metabolites with attractive bioactivities.

scholarly journals HEx: a heterologous expression platform for the discovery of fungal natural products

2018 ◽  
Author(s):  
Colin JB Harvey ◽  
Mancheng Tang ◽  
Ulrich Schlecht ◽  
Joe Horecka ◽  
Curt R Fischer ◽  
...  
Keyword(s):  
Natural Products ◽  
Synthetic Biology ◽  
Heterologous Expression ◽  
Gene Clusters ◽  
Fungal Species ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Expression Platform ◽  
The World ◽  
Fungal Natural Products

AbstractFor decades, fungi have been a source of FDA-approved natural products such as penicillin, cyclosporine, and the statins. Recent breakthroughs in DNA sequencing suggest that millions of fungal species exist on Earth with each genome encoding pathways capable of generating as many as dozens of natural products. However, the majority of encoded molecules are difficult or impossible to access because the organisms are uncultivable or the genes are transcriptionally silent. To overcome this bottleneck in natural product discovery, we developed the HEx (Heterologous EXpression) synthetic biology platform for rapid, scalable expression of fungal biosynthetic genes and their encoded metabolites in Saccharomyces cerevisiae. We applied this platform to 41 fungal biosynthetic gene clusters from diverse fungal species from around the world, 22 of which produced detectable compounds. These included novel compounds with unexpected biosynthetic origins, particularly from poorly studied species. This result establishes the HEx platform for rapid discovery of natural products from any fungal species, even those that are uncultivable, and opens the door to discovery of the next generation of natural products.SummaryHere we present the largest scale effort reported to date toward the complete refactoring and heterologous expression of fungal biosynthetic gene clusters utilizing HEx, a novel synthetic biology platform.

scholarly journals Genome Mining Uncovers Clustered Biosynthetic Pathways for Defense-Related Molecules in Bread Wheat

2021 ◽  
Author(s):  
Guy Polturak ◽  
Martin Dippe ◽  
Michael J Stephenson ◽  
Rajesh Chandra Misra ◽  
Charlotte Owen ◽  
...  
Keyword(s):  
Stress Responses ◽  
Regulatory Network ◽  
Genome Mining ◽  
Gene Clusters ◽  
Chemical Defenses ◽  
Biosynthetic Pathways ◽  
Biosynthetic Gene ◽  
Yield Losses ◽  
Biosynthetic Gene Clusters ◽  
The World

Wheat is one of the most widely grown food crops in the world. However, it succumbs to numerous pests and pathogens that cause substantial yield losses. A better understanding of biotic stress responses in wheat is thus of major importance. Here we identify previously unknown pathogen-induced biosynthetic pathways that produce a diverse set of molecules, including flavonoids, diterpenes and triterpenes. These pathways are encoded by six biosynthetic gene clusters and share a common regulatory network. We further identify associations with known or novel phytoalexin clusters in other cereals and grasses. Our results significantly advance the understanding of chemical defenses in wheat and open up new avenues for enhancing disease resistance in this agriculturally important crop.

Expanding the Natural Products Heterologous Expression Repertoire in the Model Cyanobacterium Anabaena sp. Strain PCC 7120: Production of Pendolmycin and Teleocidin B-4

2019 ◽  
Author(s):  
Patrick Videau ◽  
Kaitlyn Wells ◽  
Arun Singh ◽  
Jessie Eiting ◽  
Philip Proteau ◽  
...  
Keyword(s):  
Natural Products ◽  
Genome Mining ◽  
Gene Clusters ◽  
Combinatorial Biosynthesis ◽  
Test Case ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Cyanobacterium Anabaena ◽  
Anabaena Sp ◽  
Pcc 7120

Cyanobacteria are prolific producers of natural products and genome mining has shown that many orphan biosynthetic gene clusters can be found in sequenced cyanobacterial genomes. New tools and methodologies are required to investigate these biosynthetic gene clusters and here we present the use of <i>Anabaena </i>sp. strain PCC 7120 as a host for combinatorial biosynthesis of natural products using the indolactam natural products (lyngbyatoxin A, pendolmycin, and teleocidin B-4) as a test case. We were able to successfully produce all three compounds using codon optimized genes from Actinobacteria. We also introduce a new plasmid backbone based on the native <i>Anabaena</i>7120 plasmid pCC7120ζ and show that production of teleocidin B-4 can be accomplished using a two-plasmid system, which can be introduced by co-conjugation.

scholarly journals Global biogeographic sampling of bacterial secondary metabolism

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Zachary Charlop-Powers ◽  
Jeremy G Owen ◽  
Boojala Vijay B Reddy ◽  
Melinda A Ternei ◽  
Denise O Guimarães ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Genome Sequencing ◽  
Geographic Distance ◽  
Gene Clusters ◽  
Natural World ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Road Map ◽  
Two Factors ◽  
Natural Products Discovery

Recent bacterial (meta)genome sequencing efforts suggest the existence of an enormous untapped reservoir of natural-product-encoding biosynthetic gene clusters in the environment. Here we use the pyro-sequencing of PCR amplicons derived from both nonribosomal peptide adenylation domains and polyketide ketosynthase domains to compare biosynthetic diversity in soil microbiomes from around the globe. We see large differences in domain populations from all except the most proximal and biome-similar samples, suggesting that most microbiomes will encode largely distinct collections of bacterial secondary metabolites. Our data indicate a correlation between two factors, geographic distance and biome-type, and the biosynthetic diversity found in soil environments. By assigning reads to known gene clusters we identify hotspots of biomedically relevant biosynthetic diversity. These observations not only provide new insights into the natural world, they also provide a road map for guiding future natural products discovery efforts.

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