Lalanne et al. 2020 (PRJNA680784)
General Details
Title | Spurious regulatory connections dictate the expression-fitness landscape of translation factors |
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Organism | |
Number of Samples | 12 |
Release Date | 2020/11/25 00:00 |
Sequencing Types | |
Protocol Details |
Study Links
GWIPS-viz | Trips-Viz |
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Repository Details
SRA | SRP294161 |
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ENA | SRP294161 |
GEO | GSE162169 |
BioProject | PRJNA680784 |
Publication
Title | |
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Authors | Lalanne JB, Parker DJ, Li GW |
Journal | Molecular systems biology |
Publication Date | 2021 Apr |
Abstract | During steady-state cell growth, individual enzymatic fluxes can be directly inferred from growth rate by mass conservation, but the inverse problem remains unsolved. Perturbing the flux and expression of a single enzyme could have pleiotropic effects that may or may not dominate the impact on cell fitness. Here, we quantitatively dissect the molecular and global responses to varied expression of translation termination factors (peptide release factors, RFs) in the bacterium Bacillus subtilis. While endogenous RF expression maximizes proliferation, deviations in expression lead to unexpected distal regulatory responses that dictate fitness reduction. Molecularly, RF depletion causes expression imbalance at specific operons, which activates master regulators and detrimentally overrides the transcriptome. Through these spurious connections, RF abundances are thus entrenched by focal points within the regulatory network, in one case located at a single stop codon. Such regulatory entrenchment suggests that predictive bottom-up models of expression-fitness landscapes will require near-exhaustive characterization of parts. © 2021 The Authors. Published under the terms of the CC BY 4.0 license. |
PMC | PMC8073009 |
PMID | 33900014 |
DOI |
Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) | ||
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SRR13142690 | PRJNA680784 | Bacillus subtilis | 0.0 | 0.0 | 0.0 | ||||||||
SRR13142691 | PRJNA680784 | Bacillus subtilis | 0.0 | 0.0 | 0.0 | ||||||||
SRR13142692 | PRJNA680784 | Bacillus subtilis | 0.0 | 0.0 | 0.0 | ||||||||
SRR13142693 | PRJNA680784 | Bacillus subtilis | 0.0 | 0.0 | 0.0 | ||||||||
SRR13142694 | PRJNA680784 | Bacillus subtilis | 0.0 | 0.0 | 0.0 | ||||||||
SRR13142695 | PRJNA680784 | Bacillus subtilis | 0.0 | 0.0 | 0.0 | ||||||||
SRR13142696 | PRJNA680784 | Bacillus subtilis | 0.0 | 0.0 | 0.0 | ||||||||
SRR13142697 | PRJNA680784 | Bacillus subtilis | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR13142698 | PRJNA680784 | Bacillus subtilis | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR13142699 | PRJNA680784 | Bacillus subtilis | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR13142700 | PRJNA680784 | Bacillus subtilis | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR13142701 | PRJNA680784 | Bacillus subtilis | 0.0 | Ribo-Seq | 0.0 | ||||||||
Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) |
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