Global analysis of the specificities and targets of endoribonucleases from E. coli toxin-antitoxin systems

The purpose of this study was to identify the RNA cleavage targets and specificities of 9 endoribonuclease toxins from toxin-antitoxin systems in E. coli MG1655. This study includes 80 paired-end RNA-Seq samples. The libraries were generated from E. coli cells expressing 9 different toxins or an empty vector from an arabinose inducible promoter. The study involved 4 sets of libraries with biological duplicates of each toxin or empty vector sample for each condition totaling 20 samples for each condition. For the first condition, toxins were induced for 5 minutes and libraries were rRNA depleted and not fragmented prior to reverse transcription. These libraries were intended to identify RNA 5’-ends generated by endoribonuclease toxin cleavage. In the second condition, toxins were induced for 5 minutes and libraries were rRNA depleted and fragmented for 3 minutes prior to reverse transcription. These libraries were intended to quantify cleavage at sites identified in the first condition by measuring the loss of signal in a toxin sample relative to the empty vector control. In the third condition, toxins were induced for 5 minutes and libraries were rRNA depleted, not fragmented, and subjected to a size selection to selectively sequence cDNA arising from tRNA. These libraries were intended to determine how toxin expression altered tRNA levels. In the fourth condition, toxins were induced for 30 minutes and libraries were not rRNA depleted and were not fragmented prior to reverse transcription. These libraries were intended to determine if rRNA is cleaved or rRNA maturation is altered by toxin expression.