Abstract
Degradation of mRNA in bacteria is a regulatory mechanism, providing an efficient way to fine-tune protein abundance in response to environmental changes. While the mechanisms responsible for initiation and subsequent propagation of mRNA degradation are well studied, the mRNA features that affect its stability are yet to be elucidated. We calculated three properties for each mRNA in the E. coli transcriptome: G+C content, tRNA adaptation index (tAI) and folding energy. Each of these properties were then correlated with the experimental transcript half life measured for each transcript and detected significant correlations. A sliding window analysis identified the regions that displayed the maximal signal. The correlation between transcript half life and both G+C content and folding energy was strongest at the 5′ termini of the mRNAs. Partial correlations showed that each of the parameters contributes separately to mRNA half life. Notably, mRNAs of recently-acquired genes in the E. coli genome, which have a distinct nucleotide composition, tend to be highly stable. This high stability may aid the evolutionary fixation of horizontally acquired genes.
Highlights
The capacity to selectively degrade transcripts of different genes at different rates enhances the capability of bacteria to regulate their proteome in response to environmental changes [1,2,3]
The mechanism for mRNA degradation in Gram-negative bacteria has been extensively studied in recent years, and the enzymes that are involved in transcript degradation have been well characterized (For a review see [6]), the sequence features that determine the eventual mRNA half lives are yet to be elucidated
In order to examine whether there is a global trend that links G+C content and the stability of mRNAs in E. coli, we first calculated the G+C content of every transcript in the E. coli transcriptome
Summary
The capacity to selectively degrade transcripts of different genes at different rates enhances the capability of bacteria to regulate their proteome in response to environmental changes [1,2,3]. We correlated G+C content data with experimental half life values obtained for cells grown on a minimal medium (M9), and a rich medium (LB) in 30uC from two separate experiments (Fig. S1).
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