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Series GSE103421 Query DataSets for GSE103421
Status Public on Apr 21, 2018
Title A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation
Organisms Escherichia coli; Escherichia coli str. K-12 substr. MG1655
Experiment type Expression profiling by high throughput sequencing
Other
Summary Temperature influences the structural and functional properties of cellular components, necessitating stress responses to restore homeostasis following temperature shift. The heat shock circuitry is well understood, but 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 ORF-wide mRNA secondary structure decreases. We identified two components of an mRNA surveillance system that enable 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. Csps also remodel their own mRNAs to tune their expression to cellular need. Thus, appropriate translation is dynamically adjusted with Csp control. The universality of Csps in bacteria suggests broad utilization of this control mechanism.
 
Overall design Ribosome profiling, total RNA/mRNA-seq and DMS-seq data at 37°C and following cold shock in E. coli

Please note that the samples with _1 and _2 (in the sample titles) represent biological replicates of the same experiments.
 
Contributor(s) Zhang Y, Burkhardt DH, Rouskin S, Li G, Weissman JS, Gross CA
Citation(s) 29628307
Submission date Sep 04, 2017
Last update date Jul 25, 2021
Contact name Yan Zhang
E-mail(s) yan.jenny.zhang@gmail.com
Organization name UC San Francisco
Department Microbiology and Immunology
Lab Carol Gross
Street address 600 16th Street
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platforms (4)
GPL10328 Illumina Genome Analyzer II (Escherichia coli)
GPL14548 Illumina HiSeq 2000 (Escherichia coli)
GPL15010 Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)
Samples (55)
GSM2770989 Ribosome profiling at 37°C in WT cells_1
GSM2770990 Ribosome profiling 10 min after shift to 10°C in WT cells_1
GSM2770991 Ribosome profiling 30 min after shift to 10°C in WT cells
Relations
BioProject PRJNA401857
SRA SRP117035

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE103421_RAW.tar 289.8 Mb (http)(custom) TAR (of TXT, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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