Halves and fragments derived of tRNAs in Escherichia coli are selectively associated with 30S ribosomal subunits and in the cytosol

Abstract

The generation of tRNA halves and fragments (tsRNAs) has been associated with stressful growth conditions in eukaryotes, but reports on tsRNAs in bacteria are scarce. Here, we demonstrate that the presence of tsRNAs in Escherichia coli depends on active translation, and that they are found in the 30S ribosomal subunit and the ribosomal-free fraction, but not in the 50S subunits, 70S ribosomes or polysome fractions. However, upon dissociation into subunits at a low magnesium concentration, some of the tRNAs present in the monosomal and polysomal fractions are processed into tsRNAs. RNA-seq analyses tsRNA fractions revealed that all tRNA species in the cell were processed into fragment profiles that varied widely for each tRNA. The E. coli CP78 strain contains an unusually high concentration of tsRNAAsnGUU, but it is likely that only a fraction of this participates in translation. These tRNAs, along with others in the cell, were released from the ribosomes and processed into tsRNAs. The tRNAs in the ribosomal-free fraction appear to be cleaved by the same RNase that is active in ribosomes. We propose that tsRNAs are generated as an initial decay step for tRNAs remaining on ribosomes following translation arrest. However, tsRNAs may also have other functions.