ABSTRACT: 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.
