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Series GSE211579 Query DataSets for GSE211579
Status Public on Mar 10, 2023
Title Sodium fluoride exposure leads to ATP depletion and altered RNA decay in Escherichia coli under anaerobic conditions
Platform organism Escherichia coli str. K-12 substr. MG1655
Sample organism Escherichia coli
Experiment type Expression profiling by array
Summary We report genome-wide transcriptome profiles of E. coli obtained in the absence (control) and presence of 20 mM and 70 mM sodium fluoride (NaF) under anaerobic conditions, and assess the impact of fluoride-dependent ATP depletion on RNA turnover. We found that transcripts with increased abundance in response to NaF treatment correspond to genes that control cell envelope and osmotic stress adaptation, signal transduction systems, lipid biosynthesis, amine and polyamine degradation as well as acquisition of iron and iron homeostasis. In contrast, downregulated genes are involved in glycolysis, fatty acid metabolism, amino acid biosynthesis, energy production, cytochrome c biogenesis, protein translocation, translation, translation factors, protein folding/processing factors, transport for amino acid, sugar, or ion, and RNA metabolism.
By using a quantile-based K-means clustering approach to identify gene clusters with similar expression profiles, we identified subset (100 genes) of transcriptome whose gene expression was up- and down-regulated under fluoride and diluted fluoride conditions, respectively. In addition, we found that about 40% of the highly abundant transcripts carry repetitive extragenic palindromes (REPs). By determining the mRNA stability of osmC as well as yghA, and addressing their ribonucleases/enzymes required for RNA degradation under anaerobic conditions, we found that fluoride ions slow down RNA degradation by increasing RNA stability, in turn increasing the steady-state level of RNA. Furthermore, our results show that turnover of these REP-containing transcripts is dependent on RNase E. Collectively, our study not only reveal the effects of NaF at the whole transcriptome level under hypoxic growth conditions, but also shows that fluoride can affect gene expression post-transcriptionally by slowing down the ATP-dependent degradation of structured RNAs.
Overall design To compare the tiling array-derived transcriptome profiles of Escherichia coli with and without NaF treatment under anaerobic growth conditions
Contributor(s) Murashko ON, Yu C, Lin-Chao S
Citation(s) 36939343
Submission date Aug 18, 2022
Last update date May 11, 2023
Contact name Sue Lin-Chao
Phone 886-2-27899218
Organization name Academia Sinica
Department Institute of Molecular Biology
Lab R419
Street address 128 Academia Road, Section 2, Nankang,
City Taipei
ZIP/Postal code 11529
Country Taiwan
Platforms (1)
GPL10416 NimbleGen E. coli K12 Mg1655 385K array
Samples (18)
GSM6481068 control_rep1
GSM6481069 20 mM NaF_rep1
GSM6481070 70 mM NaF_rep1
BioProject PRJNA870936

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
GSE211579_RAW.tar 126.9 Mb (http)(custom) TAR (of PAIR, TXT)
Processed data included within Sample table
Processed data provided as supplementary file

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