Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli

RNase E, an essential endoribonuclease in Escherichia coli, is involved in 9S rRNA processing, the degradation of many mRNAs, and the processing of the M1 RNA subunit of RNase P. However, the reason that RNase E is required for cell viability is still not fully understood. In fact, recent experiments have suggested that defects in 9S rRNA processing and mRNA decay are not responsible for the lack of cell growth in RNase E mutants. By using several new rne alleles, we have confirmed these observations and have also ruled out that M1 processing by RNase E is required for cell viability. Rather, our data suggest that the critical in vivo role of RNase E is the initiation of tRNA maturation. Specifically, RNase E catalytic activity starts the processing of both polycistronic operons, such as g1yW cyst 1euZ, argX hisR 1euT proM, and 1ysT va1T 1ysW va1Z 1ysY 1ysZ 1ysQ, as well as monocistronic transcripts like pheU, pheV, asnT, asnU, asnV, and asnW, Cleavage by RNase E within a few nucleotides of the mature 3′ CCA terminus is required before RNase P and the various 3′ → 5′ exonucleases can complete tRNA maturation. All 59 tRNAs tested involved RNase E processing, although some were cleaved more efficiently than others.