Zhang et al. 2018 (PRJNA401857)

General Details

Title A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation
Organism
Number of Samples 24
Release Date 2017/09/04 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP117035
ENA SRP117035
GEO GSE103421
BioProject PRJNA401857

Publication

Title
Authors Zhang Y,Burkhardt DH,Rouskin S,Li GW,Weissman JS,Gross CA
Journal Molecular cell
Publication Date 2018 Apr 19
Abstract Temperature influences the structural and functional properties of cellular components, necessitating stress responses to restore homeostasis following temperature shift. Whereas the circuitry controlling the heat shock response is well understood, that controlling the E. coli cold shock adaptation program is not. We found that during the growth arrest phase (acclimation) that follows shift to low temperature, protein synthesis increases, and open reading frame (ORF)-wide mRNA secondary structure decreases. To identify the regulatory system controlling this process, we screened for players required for increased translation. We identified a two-member mRNA surveillance system that enables recovery of translation during acclimation: RNase R assures appropriate mRNA degradation and the Csps dynamically adjust mRNA secondary structure to globally modulate protein expression level. An autoregulatory switch in which Csps tune their own expression to cellular demand enables dynamic control of global translation. The universality of Csps in bacteria suggests broad utilization of this control mechanism. Copyright © 2018 Elsevier Inc. All rights reserved.
PMC PMC5910227
PMID 29628307
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR6001737 PRJNA401857 Escherichia coli Ribo-Seq
SRR6001738 PRJNA401857 Escherichia coli Ribo-Seq
SRR6001739 PRJNA401857 Escherichia coli Ribo-Seq
SRR6001740 PRJNA401857 Escherichia coli Ribo-Seq
SRR6001741 PRJNA401857 Escherichia coli Ribo-Seq
SRR6001742 PRJNA401857 Escherichia coli Ribo-Seq
SRR6001743 PRJNA401857 Escherichia coli Ribo-Seq
SRR6001744 PRJNA401857 Escherichia coli Ribo-Seq
SRR6001745 PRJNA401857 Escherichia coli Ribo-Seq
SRR6001746 PRJNA401857 Escherichia coli Ribo-Seq
SRR6001747 PRJNA401857 Escherichia coli Ribo-Seq
SRR6001748 PRJNA401857 Escherichia coli Ribo-Seq
SRR6001749 PRJNA401857 Escherichia coli Ribo-Seq
SRR6001750 PRJNA401857 Escherichia coli Ribo-Seq
SRR6001751 PRJNA401857 Escherichia coli RNA-Seq
SRR6001752 PRJNA401857 Escherichia coli RNA-Seq
SRR6123777 PRJNA401857 Escherichia coli RNA-Seq
SRR6507966 PRJNA401857 Escherichia coli RNA-Seq
SRR6507967 PRJNA401857 Escherichia coli RNA-Seq
SRR6507968 PRJNA401857 Escherichia coli RNA-Seq
SRR6507969 PRJNA401857 Escherichia coli RNA-Seq
SRR6507970 PRJNA401857 Escherichia coli RNA-Seq
SRR6507971 PRJNA401857 Escherichia coli RNA-Seq
SRR6507972 PRJNA401857 Escherichia coli RNA-Seq
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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