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| Status |
Public on Jul 20, 2014 |
| Title |
Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions |
| Organism |
Escherichia coli O157:H7 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Multiple infection sources for enterohemorrhagic Escherichia coli O157:H7 are known, including food of animal origin and produce. The ecology of this pathogen outside its human host is largely unknown. One third of its annotated genes still are hypothetical. To identify genetic determinants expressed under environmental factors, we applied strand-specific RNA-sequencing of strain E. coli EDL933 under 11 different biotic and abiotic conditions: LB medium at pH4, pH7, pH9, or at 15°C; LB with nitrite or trimethoprim-sulfamethoxazole; LB-agar surface, M9 minimal medium, spinach leaf juice, surface of living radish sprouts, and cattle feces. Of 5379 annotated genes, only 144 are transcriptionally completely inactive under all conditions. Of 1,771 hypothetical genes, 1,672 exhibit significant transcriptional signals under at least one condition. The pathogenicity island LEE showed highest transcriptional activity in LB medium, minimal medium, and after treatment with antibiotics. Unique sets of genes, including many hypothetical genes, are highly up regulated on radish sprouts, cattle feces, or in the presence of antibiotics. For instance, azoR is biotechnologically important, but its environmental function has been elusive. This gene is highly active on radish sprouts. Further, we observed induction of the shiga-toxin carrying phages by antibiotics and confirmed active biofilm related genes on radish sprouts, in cattle feces, and on agar plates. Thus, environmental transcriptomics uncovers hitherto unknown gene functions and regulatory patterns of Escherichia coli O157:H7.
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| Overall design |
Eleven different conditions were sequenced on the SOLiD system. Of two of the condtions, spinach medium and LB-nitrite, technical replicates were sequenced. Of LB medium and radish sprouts, biological replicates were sequenced on an Illumina MiSeq.
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| Contributor(s) |
Landstorfer RB, Simon S, Schober S, Keim D, Scherer S, Neuhaus K |
| Citation(s) |
24885796 |
| Submission date |
Jun 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard B. Landstorfer |
| E-mail(s) |
Richard.Landstorfer@wzw.tum.de
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| Organization name |
Technische Universität München
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| Department |
Chair for Microbial Ecology
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| Street address |
Weihenstephaner Berg 3
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| City |
Freising |
| ZIP/Postal code |
85354 |
| Country |
Germany |
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| Platforms (2) |
| GPL17333 |
AB SOLiD 4 System (Escherichia coli O157:H7) |
| GPL17334 |
Illumina MiSeq (Escherichia coli O157:H7) |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA209192 |
| SRA |
SRP026235 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE48199_MatrixTableGEO.xlsx.gz |
699.4 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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