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Status |
Public on Dec 19, 2022 |
Title |
Lab evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance |
Organism |
Escherichia coli str. K-12 substr. MG1655 |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
We use adaptive laboratory evolution to generate strains which tolerate high levels of the redox cycling compound paraquat, which produces reactive oxygen species (ROS). We combine resequencing, iModulon analysis of the transcripome, and metabolic models to elucidate six interacting stress tolerance mechanisms: 1) modification of transport, 2) activation of ROS stress responses, 3) use of ROS-sensitive iron regulation, 4) motility, 5) broad transcriptional reallocation toward growth, and 6) metabolic rewiring to decrease NADH production. This work thus reveals the genome-scale systems biology of ROS tolerance.
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Overall design |
Tolerization adaptive laboratory evolution (ALE) to increase paraquat. We started with GLU4 (0_0), a strain of E. coli MG1655 which was media-adapted using ALE in LaCroix et al. 2015 (doi: 10.1128/AEM.02246-14). We then evolved it with increasing PQ concentrations over 33 days in triplicate, generating strains 1_0, 2_0, and 3_0. Following that, 11 more strains were generated using a second gerenation of ALE for up to 55 days in a hierarchy, with 1_1, 1_2, ... descending from 1_0; 2_1, 2_2, ... descending from 2_0, and so on. Data from 0_0, 1_0, and 2_0 are available at GEO accession number GSE134256. See http://aledb.org/stats/?ale_experiment_id=1540 for the sets of mutations for all strains. Each evolved strain was cultured in M9 minimal media with 0.4% w/v glucose to an OD of 0.025 then exposed to 0, 250, or 750 uM paraquat for 20 minutes prior to RNA collection. These samples were also included in PRECISE-1K, a dataset which can be explored on iModulonDB.org.
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Contributor(s) |
Rychel K, Tan J, Palsson B |
Citation(s) |
37713311 |
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Submission date |
Dec 19, 2022 |
Last update date |
Nov 13, 2023 |
Contact name |
Kevin Rychel |
E-mail(s) |
krychel@eng.ucsd.edu
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Phone |
2244367353
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Organization name |
University of California San Diego
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Department |
Bioengineering
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Lab |
Systems Biology Research Group
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Street address |
9500 Gilman Dr
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City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92093 |
Country |
USA |
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Platforms (1) |
GPL24659 |
Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655) |
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Samples (84)
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Relations |
BioProject |
PRJNA913892 |
Supplementary file |
Size |
Download |
File type/resource |
GSE221314_RAW.tar |
3.0 Mb |
(http)(custom) |
TAR (of CSV) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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