A Genome-Wide Mutant Library of Pseudomonas aeruginosa

Pseudomonas aeruginosa (PA) is an opportunistic pathogen that causes diverse human infections including chronic airway infection in patients with cystic fibrosis (CF). Comparing the genomes of CF and non-CF PA isolates has great potential to identify the genetic basis of pathogenicity. To gain a deeper understanding of PA adaptation in CF airways, we performed a genome-wide association study (GWAS) on 1,001 PA genomes. Genetic variations identified among CF isolates were categorized into (i) alterations in protein-coding regions, either large- or small-scale, and (ii) polymorphic variation in intergenic regions. We introduced each CF-associated genetic alteration into the genome of PAO1, a prototype PA strain, and validated the outcomes experimentally. Loci readily mutated among CF isolates included genes encoding a probable sulfatase, a probable TonB-dependent receptor (PA2332~PA2336), L-cystine transporter (YecS, PA0313), and a probable transcriptional regulator (PA5438). A promoter region of a heme/hemoglobin uptake outer membrane receptor (PhuR, PA4710) was also different between the CF and non-CF isolate groups. Our analysis highlights ways in which the PA genome evolves to survive and persist within the context of chronic CF infection.

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A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis

Nature Genetics ◽

10.1038/s41588-019-0370-6 ◽

2019 ◽

Vol 51 (4) ◽

pp. 627-635 ◽

Cited By ~ 42

Author(s):

Xiaobo Li ◽

Weronika Patena ◽

Friedrich Fauser ◽

Robert E. Jinkerson ◽

Shai Saroussi ◽

...

Keyword(s):

Mutant Library ◽

Functional Screen ◽

Genome Wide ◽

A Genome

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Towards a Systems Approach in the Genetic Analysis of Archaea: Accelerating Mutant Construction and Phenotypic Analysis inHaloferax volcanii

Archaea ◽

10.1155/2010/426239 ◽

2010 ◽

Vol 2010 ◽

pp. 1-11 ◽

Cited By ~ 22

Author(s):

Ian K. Blaby ◽

Gabriela Phillips ◽

Crysten E. Blaby-Haas ◽

Kevin S. Gulig ◽

Basma El Yacoubi ◽

...

Keyword(s):

High Throughput ◽

Gene Deletion ◽

Systems Approach ◽

Essential Gene ◽

Gene Knockout ◽

Deletion Mutants ◽

Mutant Library ◽

Phenotypic Analysis ◽

Genome Wide ◽

A Genome

With the availability of a genome sequence and increasingly sophisticated genetic tools,Haloferax volcaniiis becoming a model for both Archaea and halophiles. In order forH. volcaniito reach a status equivalent toEscherichia coli, Bacillus subtilis, orSaccharomyces cerevisiae, a gene knockout collection needs to be constructed in order to identify the archaeal essential gene set and enable systematic phenotype screens. A streamlined gene-deletion protocol adapted for potential automation was implemented and used to generate 22H. volcaniideletion strains and identify several potentially essential genes. These gene deletion mutants, generated in this and previous studies, were then analyzed in a high-throughput fashion to measure growth rates in different media and temperature conditions. We conclude that these high-throughput methods are suitable for a rapid investigation of anH. volcaniimutant library and suggest that they should form the basis of a larger genome-wide experiment.

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Genome-Scale Screening of Vaccine Candidates Against Pseudomonas Aeruginosa

10.21203/rs.3.rs-89769/v1 ◽

2020 ◽

Author(s):

Chuang Wan ◽

Chen Gao ◽

Qin Xie ◽

Yin Wang ◽

Xin Cheng ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Protective Antigen ◽

Bacterial Load ◽

Protective Antigens ◽

Genome Wide ◽

A Genome ◽

New Strategy ◽

Opsonophagocytic Killing ◽

Genome Scale

Abstract BackgroundInfections due to Pseudomonas aeruginosa (PA) are becoming a serious threat to patients in intensive care units. A PA vaccine is a practical and economical solution to solve the problems caused by PA infection successfully. In recent years, several antigen candidates have been tested in animal and human clinical trials, but none of them has been approved to date. An alternative strategy for antigen screening and protective antigens is in urgent demand.MethodsIn this study, we generated a genome-wide library of PA protein fragments tagged with maltose-binding protein (MBP). Using sera from patients who recovered after PA infection, we identified novel protective antigens and investigate the mechanism of these antigens induced protections.Resultswe identified a novel protective antigen, FlgE, which is the structural component of the flagella hook. Vaccination with recombinant FlgE (reFlgE) induced a Th2-predominant immune response and reduced bacterial load and inflammation in PA-infected mice. Anti-reFlgE antibodies recognized native FlgE on the bacterial membrane in vitro and conferred protection in mice, which may be due to the mediation of opsonophagocytic killing and inhibition of bacterial motility. In addition, the combination of reFlgE with rePcrVNH, an engineered antigen we reported previously, provided elevated protection against PA infection.ConclusionOur data demonstrate that FlgE is a promising vaccine candidate for PA and provide a new strategy for the efficient screening of antigens of other pathogens.

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A Genome-Wide, Mapped Algal Mutant Library Enables High-Throughput Genetic Studies in a Photosynthetic Eukaryote

SSRN Electronic Journal ◽

10.2139/ssrn.3155767 ◽

2018 ◽

Author(s):

Xiaobo Li ◽

Weronika Patena ◽

Friedrich Fauser ◽

Robert E. Jinkerson ◽

Shai Saroussi ◽

...

Keyword(s):

High Throughput ◽

Mutant Library ◽

Photosynthetic Eukaryote ◽

Genetic Studies ◽

Genome Wide ◽

A Genome

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A Robust Genome-Wide Association Study Uncovers Signature Genetic Alterations among Pseudomonas aeruginosa Cystic Fibrosis Isolates

10.1101/2020.12.02.407528 ◽

2020 ◽

Author(s):

Wontae Hwang ◽

Ji Hyun Yong ◽

Kyung Bae Min ◽

Kang-Mu Lee ◽

Sang Sun Yoon

Keyword(s):

Cystic Fibrosis ◽

Pseudomonas Aeruginosa ◽

Association Study ◽

Genome Wide Association Study ◽

Genetic Alterations ◽

Genome Wide Association ◽

Small Scale ◽

Outer Membrane Receptor ◽

Genome Wide ◽

A Genome

AbstractPseudomonas aeruginosa (PA) is an opportunistic pathogen that causes diverse human infections such as chronic airway infection in cystic fibrosis (CF) patients. Although many sequenced genomes are available, a comprehensive comparison between genomes of CF versus non-CF PA isolates remains yet to be conducted. In order to gain a deeper understanding into the PA adaptation in the CF airway, we performed a Genome-Wide Association Study (GWAS) using a total of 1,001 PA genomes. Genetic variations uniquely identified among CF isolates were categorized into (i) alterations in protein-coding regions either large- or small-scale and (ii) polymorphic variations in intergenic regions. We introduced each CF-specific genetic alteration into the genome of PAO1, a prototype PA strain and experimentally validated their outcomes. Loci readily mutated among CF isolates include genes encoding a probable sulphatase and a probable TonB-dependent receptor (PA2332~PA2336), L-cysteine transporter (YecS, PA0313) and a probable transcriptional regulator (PA5438). A promoter region of heme/hemoglobin uptake outer membrane receptor (PhuR, PA4710) was similarly identified as meaningfully different between the CF and non-CF isolate groups. Our analysis, the first of its kind, highlights how PA evolves its genome to persist and survive within the context of chronic CF infection.

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