NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE221314 Query DataSets for GSE221314
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
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.
 
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.
 
Contributor(s) Rychel K, Tan J, Palsson B
Citation(s) 37713311
Submission date Dec 19, 2022
Last update date Nov 13, 2023
Contact name Kevin Rychel
E-mail(s) krychel@eng.ucsd.edu
Phone 2244367353
Organization name University of California San Diego
Department Bioengineering
Lab Systems Biology Research Group
Street address 9500 Gilman Dr
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platforms (1)
GPL24659 Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)
Samples (84)
GSM6858240 1_0_750pq__1
GSM6858241 1_0_750pq__2
GSM6858242 1_1_0pq__1
Relations
BioProject PRJNA913892

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE221314_RAW.tar 3.0 Mb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap