 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 06, 2016 |
| Title |
Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification |
| Organism |
Escherichia coli |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Escherichia coli spans a genetic continuum from enteric strains to several phylogenetically distinct, atypical lineages that are rare in humans, but more common in extra-intestinal environments. To investigate the link between gene regulation, phylogeny and diversification in this species, we analyzed global gene expression profiles of four strains representing distinct evolutionary lineages, including a well-studied laboratory strain, a typical commensal (enteric) strain and two environmental strains. RNA-Seq was employed to compare the whole transcriptomes of strains grown under batch, chemostat and starvation conditions. Highly differentially expressed genes showed a significantly lower nucleotide sequence identity compared with other genes, indicating that gene regulation and coding sequence conservation are directly connected. Overall, distances between the strains based on gene expression profiles were largely dependent on the culture condition and did not reflect phylogenetic relatedness. Expression differences of commonly shared genes (all four strains) and E. coli core genes were consistently smaller between strains characterized by more similar primary habitats. For instance, environmental strains exhibited increased expression of stress defense genes under carbon-limited growth and entered a more pronounced survival-like phenotype during starvation compared with other strains, which stayed more alert for substrate scavenging and catabolism during no-growth conditions. Since those environmental strains show similar genetic distance to each other and to the other two strains, these findings cannot be simply attributed to genetic relatedness but suggest physiological adaptations. Our study provides new insights into ecologically relevant gene-expression and underscores the role of (differential) gene regulation for the diversification of the model bacterial species.
|
| |
|
| Overall design |
Four E.coli strains, laboratory strain K12 (MG1655), a commensal model strain (IAI1), a soil-isolated strain (TW11588-Clade IV), and a freshwater-isolated strain (TW09308—Clade V) were used. Each strain was grown on a minimal growth medium (Ihssen and Egli, 2004) in three treatment modes: chemostat, batch, and starvation. Cells from batch culture were collected when reaching steady-state. For starvation, the medium flow was stopped during steady-state and bacteria were collected after 4 h.
|
| |
|
| Contributor(s) |
Vital M, Chai B, Østman B, Cole JR, Konstantinidis KT, Tiedje JM |
| Citation(s) |
25343512 |
| |
| Submission date |
Jan 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Benli Chai |
| E-mail(s) |
chaibenl@msu.edu
|
| Phone |
517-353-3842
|
| Organization name |
Michigan State University
|
| Department |
Center for Microbial Ecology
|
| Street address |
567 Wilson Road Rm 2225 A
|
| City |
East Lansing |
| State/province |
Michigan |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL14548 |
Illumina HiSeq 2000 (Escherichia coli) |
|
| Samples (24)
|
| GSM2049254 |
MG1655 transcriptome from chemostat growth_1 |
| GSM2049255 |
MG1655 transcriptome from batch growth_1 |
| GSM2049256 |
MG1655 transcriptome from starvation growth_1 |
| GSM2049257 |
IAI1 transcriptome from chemostat growth_1 |
| GSM2049258 |
IAI1 transcriptome from batch growth_1 |
| GSM2049259 |
IAI1 transcriptome from starvation growth_1 |
| GSM2049260 |
TW11588 transcriptome from chemostat growth_1 |
| GSM2049261 |
TW11588 transcriptome from batch growth_1 |
| GSM2049262 |
TW11588 transcriptome from starvation growth_1 |
| GSM2049263 |
TW09308 transcriptome from chemostat growth_1 |
| GSM2049264 |
TW09308 transcriptome from batch growth_1 |
| GSM2049265 |
TW09308 transcriptome from starvation growth_1 |
| GSM2049266 |
MG1655 transcriptome from chemostat growth_2 |
| GSM2049267 |
MG1655 transcriptome from batch growth_2 |
| GSM2049268 |
MG1655 transcriptome from starvation growth_2 |
| GSM2049269 |
IAI1 transcriptome from chemostat growth_2 |
| GSM2049270 |
IAI1 transcriptome from batch growth_2 |
| GSM2049271 |
IAI1 transcriptome from starvation growth_2 |
| GSM2049272 |
TW11588 transcriptome from chemostat growth_2 |
| GSM2049273 |
TW11588 transcriptome from batch growth_2 |
| GSM2049274 |
TW11588 transcriptome from starvation growth_2 |
| GSM2049275 |
TW09308 transcriptome from chemostat growth_2 |
| GSM2049276 |
TW09308 transcriptome from batch growth_2 |
| GSM2049277 |
TW09308 transcriptome from starvation growth_2 |
|
| Relations |
| BioProject |
PRJNA310115 |
| SRA |
SRP069023 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE77325_Gene_annotations.txt.gz |
157.4 Kb |
(ftp)(http) |
TXT |
| GSE77325_normalized_count.txt.gz |
756.6 Kb |
(ftp)(http) |
TXT |
| GSE77325_panGeneMap.txt.gz |
197.8 Kb |
(ftp)(http) |
TXT |
| GSE77325_raw_count.txt.gz |
186.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...