Lalanne et al. 2020 (PRJNA680784)

General Details

Title Spurious regulatory connections dictate the expression-fitness landscape of translation factors
Organism
Number of Samples 12
Release Date 2020/11/25 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP294161
ENA SRP294161
GEO GSE162169
BioProject PRJNA680784

Publication

Title
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)
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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