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.

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.

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 Rational construction of genome-reduced Burkholderiales chassis facilitates efficient heterologous production of natural products from proteobacteria

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jiaqi Liu ◽  
Haibo Zhou ◽  
Zhiyu Yang ◽  
Xue Wang ◽  
Hanna Chen ◽  
...  
Keyword(s):  
Natural Products ◽  
Heterologous Expression ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Wild Type ◽  
Biosynthetic Gene Clusters ◽  
Gram Negative ◽  
Cell Autolysis ◽  
Rational Construction ◽  
Genomic Regions

AbstractHeterologous expression of biosynthetic gene clusters (BGCs) avails yield improvements and mining of natural products, but it is limited by lacking of more efficient Gram-negative chassis. The proteobacterium Schlegelella brevitalea DSM 7029 exhibits potential for heterologous BGC expression, but its cells undergo early autolysis, hindering further applications. Herein, we rationally construct DC and DT series genome-reduced S. brevitalea mutants by sequential deletions of endogenous BGCs and the nonessential genomic regions, respectively. The DC5 to DC7 mutants affect growth, while the DT series mutants show improved growth characteristics with alleviated cell autolysis. The yield improvements of six proteobacterial natural products and successful identification of chitinimides from Chitinimonas koreensis via heterologous expression in DT mutants demonstrate their superiority to wild-type DSM 7029 and two commonly used Gram-negative chassis Escherichia coli and Pseudomonas putida. Our study expands the panel of Gram-negative chassis and facilitates the discovery of natural products by heterologous expression.

scholarly journals Draft Genome Sequence of Bacillus sp. Strain M21, Isolated from the Arid Area of Matmata, Tunisia

2018 ◽  
Vol 6 (17) ◽  
Author(s):  
Zina Nasfi ◽  
Anja Poehlein ◽  
Henrik Harms ◽  
Emilie Goralski ◽  
Katja M. Fisch ◽  
...  
Keyword(s):  
Draft Genome ◽  
Gene Clusters ◽  
Arid Area ◽  
Bacillus Sp ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Total Size ◽  
Gram Negative ◽  
Content Type ◽  
Specialized Metabolites

ABSTRACT Bacillus sp. strain M21 was isolated from an environmental sample. In antibacterial screenings, the strain inhibited growth of Gram-positive and Gram-negative test strains. The genome was assembled into 69 contigs with a total size of 5.178 Mb. The strain contains at least nine biosynthetic gene clusters for the production of specialized metabolites.

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.

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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