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

Abstract

Almost all elongator tRNAs (Transfer RNAs) harbor 5-methyluridine 54 and pseudouridine 55 in the T arm, generated by the enzymes TrmA and TruB, respectively, in <i>Escherichia coli.</i> TrmA and TruB both act as tRNA chaperones, and strains lacking <i>trmA</i> or <i>truB</i> are outcompeted by wild type. Here, we investigate how TrmA and TruB contribute to cellular fitness. Deletion of <i>trmA</i> and <i>truB</i> in <i>E. coli</i> causes a global decrease in aminoacylation and alters other tRNA modifications such as acp³U47. While overall protein synthesis is not affected in <i>Δ</i><i>trmA</i> and <i>Δ</i><i>truB</i> strains, the translation of a subset of codons is significantly impaired. As a consequence, we observe translationally reduced expression of many specific proteins, that are either encoded with a high frequency of these codons or that are large proteins. The resulting proteome changes are not related to a specific growth phenotype, but overall cellular fitness is impaired upon deleting <i>trmA</i> and <i>truB</i> in accordance with a general protein synthesis impact. In conclusion, we demonstrate that universal modifications of the tRNA T arm are critical for global tRNA function by enhancing tRNA maturation, tRNA aminoacylation, and translation, thereby improving cellular fitness irrespective of the growth conditions which explains the conservation of <i>trmA</i> and <i>truB</i>.