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| Status |
Public on Aug 07, 2023 |
| Title |
The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions |
| Organism |
Escherichia coli K-12 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Fit phenotypes are achieved through optimal transcriptomic allocation. Here, we performed a high-resolution, multi-scale study of the transcriptomic tradeoff between two key fitness phenotypes, stress response (fear) and growth (greed), in Escherichia coli. We introduced 12 RNA polymerase (RNAP) mutations commonly acquired during adaptive laboratory evolution (ALE) and found that single mutations could result in large shifts in this fear vs. greed tradeoff likely through destabilizing the rpoB-rpoC interface. RpoS and GAD regulons drive the fear response while ribosomal proteins and the ppGpp regulon underlie greed. Growth rate selection pressure during ALE results in endpoint strains that universally have RNAP mutations, with synergistic mutations reflective of particular conditions. A phylogenetic analysis found the tradeoff in numerous bacteria species and one archaea species. The results suggest that the tradeoff represents a general principle of transcriptome allocation in bacteria where small genetic changes can result in large phenotypic adaptations to growth conditions.
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| Overall design |
RNA-sequencing of RNAP single mutation strains using Qiagen RNA-protect bacteria reagant, Zymo Rsearch Quick-RNA MicroPrep Kit and Kapa Biosystems RNA HyperPrep
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| Contributor(s) |
Dalldorf C, Rychel K, Szubin R, Hefner Y, Patel A, Zielinski D, Palsson B |
| Citation(s) |
37090546 |
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| Submission date |
Mar 17, 2023 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Christopher Dalldorf |
| E-mail(s) |
cdalldor@eng.ucsd.edu
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| Organization name |
UCSD
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| Department |
Bioengineering
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| Lab |
SBRG, Palsson
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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) |
| GPL26856 |
Illumina NovaSeq 6000 (Escherichia coli K-12) |
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| Samples (38)
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| Relations |
| BioProject |
PRJNA945925 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE227624_counts.csv.gz |
257.2 Kb |
(ftp)(http) |
CSV |
| GSE227624_log_tpm.csv.gz |
1.3 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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