Modifications in the T arm of tRNA globally determine tRNA function and cellular fitness

All elongator tRNAs harbor 5-methyluridine at position 54 and pseudouridine at position 55 in the T arm, which are generated by the enzymes TrmA and TruB, respectively. Escherichia coli TrmA and TruB have both been shown to act as tRNA chaperones, and strains lacking trmA or truB are outcompeted by wildtype. Here, we investigate how TrmA and TruB contribute to cellular fitness. Deletion of trmA and truB in E. coli causes a global decrease in aminoacylation and alters other tRNA modification such as acp3U47 and 4-thiouridine. Whereas global protein synthesis is not significantly changed in ΔtrmA and ΔtruB, the expression of many specific proteins is altered at the translational level. In conclusion, we demonstrate that universal modifications of the tRNA T arm are critical for global tRNA function by enhancing other tRNA modifications, tRNA folding, tRNA aminoacylation, and translation of specific genes thereby improving cellular fitness and explaining their conservation. To examine how mRNA levels compare between Escherichia coli lacking trmA, truB, or both trmA and truB genes and the parental E. coli BW25113 strain, we extracted total RNA from each strain after growth in LB + 2% sodium formate to an OD600 between 0.3 and 0.4 using TRIzol. Three biological replicates were performed for each strain.