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DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli

BACKGROUND: During infection of the urinary tract, uropathogenic Escherichia coli (UPEC) are exposed to different environments, such as human urine and the intracellular environments of bladder epithelial cells. Each environment elicits a distinct bacterial environment-specific transcriptional respo...

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Autores principales: Madelung, Michelle, Kronborg, Tina, Doktor, Thomas Koed, Struve, Carsten, Krogfelt, Karen Angeliki, Møller-Jensen, Jakob
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5404293/
https://www.ncbi.nlm.nih.gov/pubmed/28438119
http://dx.doi.org/10.1186/s12866-017-1008-4
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author Madelung, Michelle
Kronborg, Tina
Doktor, Thomas Koed
Struve, Carsten
Krogfelt, Karen Angeliki
Møller-Jensen, Jakob
author_facet Madelung, Michelle
Kronborg, Tina
Doktor, Thomas Koed
Struve, Carsten
Krogfelt, Karen Angeliki
Møller-Jensen, Jakob
author_sort Madelung, Michelle
collection PubMed
description BACKGROUND: During infection of the urinary tract, uropathogenic Escherichia coli (UPEC) are exposed to different environments, such as human urine and the intracellular environments of bladder epithelial cells. Each environment elicits a distinct bacterial environment-specific transcriptional response. We combined differential fluorescence induction (DFI) with next-generation sequencing, collectively termed DFI-seq, to identify differentially expressed genes in UPEC strain UTI89 during growth in human urine and bladder cells. RESULTS: DFI-seq eliminates the need for iterative cell sorting of the bacterial library and yields a genome-wide view of gene expression. By analysing the gene expression of UPEC in human urine we found that genes involved in amino acid biosynthesis were upregulated. Deletion mutants lacking genes involved in arginine biosynthesis were outcompeted by the wild type during growth in human urine and inhibited in their ability to invade or proliferate in the J82 bladder epithelial cell line. Furthermore, DFI-seq was used to identify genes involved in invasion of J82 bladder epithelial cells. 56 genes were identified to be differentially expressed of which almost 60% encoded hypothetical proteins. One such gene UTI89_C5139, displayed increased adhesion and invasion of J82 cells when deleted from UPEC strain UTI89. CONCLUSIONS: We demonstrate the usefulness of DFI-seq for identification of genes required for optimal growth of UPEC in human urine, as well as potential virulence genes upregulated during infection of bladder cell culture. DFI-seq holds potential for the study of bacterial gene expression in live-animal infection systems. By linking fitness genes, such as those genes involved in amino acid biosynthesis, to virulence, this study contributes to our understanding of UPEC pathophysiology. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12866-017-1008-4) contains supplementary material, which is available to authorized users.
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spelling pubmed-54042932017-04-27 DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli Madelung, Michelle Kronborg, Tina Doktor, Thomas Koed Struve, Carsten Krogfelt, Karen Angeliki Møller-Jensen, Jakob BMC Microbiol Research Article BACKGROUND: During infection of the urinary tract, uropathogenic Escherichia coli (UPEC) are exposed to different environments, such as human urine and the intracellular environments of bladder epithelial cells. Each environment elicits a distinct bacterial environment-specific transcriptional response. We combined differential fluorescence induction (DFI) with next-generation sequencing, collectively termed DFI-seq, to identify differentially expressed genes in UPEC strain UTI89 during growth in human urine and bladder cells. RESULTS: DFI-seq eliminates the need for iterative cell sorting of the bacterial library and yields a genome-wide view of gene expression. By analysing the gene expression of UPEC in human urine we found that genes involved in amino acid biosynthesis were upregulated. Deletion mutants lacking genes involved in arginine biosynthesis were outcompeted by the wild type during growth in human urine and inhibited in their ability to invade or proliferate in the J82 bladder epithelial cell line. Furthermore, DFI-seq was used to identify genes involved in invasion of J82 bladder epithelial cells. 56 genes were identified to be differentially expressed of which almost 60% encoded hypothetical proteins. One such gene UTI89_C5139, displayed increased adhesion and invasion of J82 cells when deleted from UPEC strain UTI89. CONCLUSIONS: We demonstrate the usefulness of DFI-seq for identification of genes required for optimal growth of UPEC in human urine, as well as potential virulence genes upregulated during infection of bladder cell culture. DFI-seq holds potential for the study of bacterial gene expression in live-animal infection systems. By linking fitness genes, such as those genes involved in amino acid biosynthesis, to virulence, this study contributes to our understanding of UPEC pathophysiology. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12866-017-1008-4) contains supplementary material, which is available to authorized users. BioMed Central 2017-04-24 /pmc/articles/PMC5404293/ /pubmed/28438119 http://dx.doi.org/10.1186/s12866-017-1008-4 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Madelung, Michelle
Kronborg, Tina
Doktor, Thomas Koed
Struve, Carsten
Krogfelt, Karen Angeliki
Møller-Jensen, Jakob
DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli
title DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli
title_full DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli
title_fullStr DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli
title_full_unstemmed DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli
title_short DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli
title_sort dfi-seq identification of environment-specific gene expression in uropathogenic escherichia coli
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5404293/
https://www.ncbi.nlm.nih.gov/pubmed/28438119
http://dx.doi.org/10.1186/s12866-017-1008-4
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