DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli
Abstract 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 transcription...
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doaj-6de662c659234a74a24f71792a59055b2020-11-25T00:47:06ZengBMCBMC Microbiology1471-21802017-04-0117111910.1186/s12866-017-1008-4DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coliMichelle Madelung0Tina Kronborg1Thomas Koed Doktor2Carsten Struve3Karen Angeliki Krogfelt4Jakob Møller-Jensen5Department of Biochemistry and Molecular Biology, University of Southern DenmarkDepartment of Biochemistry and Molecular Biology, University of Southern DenmarkDepartment of Biochemistry and Molecular Biology, University of Southern DenmarkDepartment of Microbiology and Infection Control, Statens Serum InstitutDepartment of Microbiology and Infection Control, Statens Serum InstitutDepartment of Biochemistry and Molecular Biology, University of Southern DenmarkAbstract 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.http://link.springer.com/article/10.1186/s12866-017-1008-4DFINGSUPECAmino acid biosynthesisVirulenceUTI |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Michelle Madelung Tina Kronborg Thomas Koed Doktor Carsten Struve Karen Angeliki Krogfelt Jakob Møller-Jensen |
spellingShingle |
Michelle Madelung Tina Kronborg Thomas Koed Doktor Carsten Struve Karen Angeliki Krogfelt Jakob Møller-Jensen DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli BMC Microbiology DFI NGS UPEC Amino acid biosynthesis Virulence UTI |
author_facet |
Michelle Madelung Tina Kronborg Thomas Koed Doktor Carsten Struve Karen Angeliki Krogfelt Jakob Møller-Jensen |
author_sort |
Michelle Madelung |
title |
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_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_sort |
dfi-seq identification of environment-specific gene expression in uropathogenic escherichia coli |
publisher |
BMC |
series |
BMC Microbiology |
issn |
1471-2180 |
publishDate |
2017-04-01 |
description |
Abstract 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. |
topic |
DFI NGS UPEC Amino acid biosynthesis Virulence UTI |
url |
http://link.springer.com/article/10.1186/s12866-017-1008-4 |
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