Difference between revisions of "PMID:18833300"

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'''Johnson, DA , Tetu, SG , Phillippy, K , Chen, J , Ren, Q  and Paulsen, IT '''  (2008) High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes. ''PLoS Genet.'' '''4''':e1000211
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!align=left  |Abstract
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The deluge of data generated by genome sequencing has led to an increasing reliance on bioinformatic predictions, since the traditional experimental approach of characterizing gene function one at a time cannot possibly keep pace with the sequence-based discovery of novel genes. We have utilized Biolog phenotype MicroArrays to identify phenotypes of gene knockout mutants in the opportunistic pathogen and versatile soil bacterium Pseudomonas aeruginosa in a relatively high-throughput fashion. Seventy-eight P. aeruginosa mutants defective in predicted sugar and amino acid membrane transporter genes were screened and clear phenotypes were identified for 27 of these. In all cases, these phenotypes were confirmed by independent growth assays on minimal media. Using qRT-PCR, we demonstrate that the expression levels of 11 of these transporter genes were induced from 4- to 90-fold by their substrates identified via phenotype analysis. Overall, the experimental data showed the bioinformatic predictions to be largely correct in 22 out of 27 cases, and led to the identification of novel transporter genes and a potentially new histamine catabolic pathway. Thus, rapid phenotype identification assays are an invaluable tool for confirming and extending bioinformatic predictions.
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18833300 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2542419 PMC2542419]
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Online version:[http://dx.doi.org/10.1371/journal.pgen.1000211 10.1371/journal.pgen.1000211]
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Bacterial Proteins/genetics; Bacterial Proteins/metabolism; Computational Biology/methods; Membrane Transport Proteins/genetics; Membrane Transport Proteins/metabolism; Mutagenesis, Insertional; Phenotype; Protein Array Analysis; Pseudomonas aeruginosa/genetics; Pseudomonas aeruginosa/growth & development; Pseudomonas aeruginosa/metabolism
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==Main Points of the Paper ==
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== Materials and Methods Used ==
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==Phenotype Annotations==
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==Notes==
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==References==
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[[Category:Publication]]

Revision as of 11:33, 17 September 2012

Citation

Johnson, DA , Tetu, SG , Phillippy, K , Chen, J , Ren, Q and Paulsen, IT (2008) High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes. PLoS Genet. 4:e1000211

Abstract

The deluge of data generated by genome sequencing has led to an increasing reliance on bioinformatic predictions, since the traditional experimental approach of characterizing gene function one at a time cannot possibly keep pace with the sequence-based discovery of novel genes. We have utilized Biolog phenotype MicroArrays to identify phenotypes of gene knockout mutants in the opportunistic pathogen and versatile soil bacterium Pseudomonas aeruginosa in a relatively high-throughput fashion. Seventy-eight P. aeruginosa mutants defective in predicted sugar and amino acid membrane transporter genes were screened and clear phenotypes were identified for 27 of these. In all cases, these phenotypes were confirmed by independent growth assays on minimal media. Using qRT-PCR, we demonstrate that the expression levels of 11 of these transporter genes were induced from 4- to 90-fold by their substrates identified via phenotype analysis. Overall, the experimental data showed the bioinformatic predictions to be largely correct in 22 out of 27 cases, and led to the identification of novel transporter genes and a potentially new histamine catabolic pathway. Thus, rapid phenotype identification assays are an invaluable tool for confirming and extending bioinformatic predictions.

Links

PubMed PMC2542419 Online version:10.1371/journal.pgen.1000211

Keywords

Bacterial Proteins/genetics; Bacterial Proteins/metabolism; Computational Biology/methods; Membrane Transport Proteins/genetics; Membrane Transport Proteins/metabolism; Mutagenesis, Insertional; Phenotype; Protein Array Analysis; Pseudomonas aeruginosa/genetics; Pseudomonas aeruginosa/growth & development; Pseudomonas aeruginosa/metabolism

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Main Points of the Paper

Please summarize the main points of the paper.

Materials and Methods Used

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Phenotype Annotations

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Phenotype of Taxon Information Genotype Information (if known) Condition Information OMP ID OMP Term Name ECO ID ECO Term Name Notes Status
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Notes

References

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