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

Abstract

All elongator tRNAs harbor 5-methyluridine 54 and pseudouridine 55 in the T arm, which are generated by the enzymes TrmA and TruB, respectively.Escherichia coliTrmA and TruB both act as tRNA chaperones, and strains lackingtrmAortruBare outcompeted by wildtype. Here, we investigate how TrmA and TruB contribute to cellular fitness. Deletion oftrmAandtruBinE. colicauses a global decrease in aminoacylation and alters other tRNA modification such as acp3U47. Whereas overall protein synthesis is not affected in ΔtrmAand ΔtruBstrains, the translation of a specific subset of codons is significantly impaired, and the expression of many specific proteins is translationally changed. 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 and explainingtrmAandtruBconservation.

Beyond the Anticodon: tRNA Core Modifications and Their Impact on Structure, Translation and Stress Adaptation

“… Modification circuits involving tRNA core modifications: ( a ) modification circuits identified in T. thermophilus in response to temperature changes represented on a cloverleaf scheme [ 94 , 95 , 107 ]; ( b ) T-arm modification circuits identified in yeast [ 69 , 70 ]; ( c , d ) modification circuits identified in E. coli [ 109 , 110 , 111 ]; and ( e ) modification circuits identified in E. coli [ 111 ]. Modifications are represented by colored circles (see the legend in the box for the corresponding colors).…”

“…Recently, several reports have shed light on modification cross-talks among tRNA core modifications in E. coli . They reported that the introduction of U47 is globally enhanced by the prior presence of m 7 G46 [ 109 ] and also stimulated by m 5 U54 in E. coli , , , and [ 110 , 111 ] ( Figure 3 c). 55 seems to also participate in this network, in which it may either slightly stimulate or inhibit the introduction of U47 in E. coli and , respectively [ 111 ].…”

“…They reported that the introduction of U47 is globally enhanced by the prior presence of m 7 G46 [ 109 ] and also stimulated by m 5 U54 in E. coli , , , and [ 110 , 111 ] ( Figure 3 c). 55 seems to also participate in this network, in which it may either slightly stimulate or inhibit the introduction of U47 in E. coli and , respectively [ 111 ]. In addition, the formation of ms 2 A37 in the ACL of E. coli is activated by m 5 U54 [ 110 , 111 ] ( Figure 3 d), and the introduction of s 4 U8 is enhanced in the presence of 55 and m 5 U54 in E. coli [ 111 ] ( Figure 3 e).…”

“… 55 seems to also participate in this network, in which it may either slightly stimulate or inhibit the introduction of U47 in E. coli and , respectively [ 111 ]. In addition, the formation of ms 2 A37 in the ACL of E. coli is activated by m 5 U54 [ 110 , 111 ] ( Figure 3 d), and the introduction of s 4 U8 is enhanced in the presence of 55 and m 5 U54 in E. coli [ 111 ] ( Figure 3 e). These interdependencies in E. coli tRNA core modifications were identified using a combination of nucleotide quantification and sequencing techniques, such as HPLC, liquid-chromatography coupled to tandem mass spectrometry (LC-MS/MS), multiplex small RNA-sequencing (MSR-seq) and primer extension analysis.…”

“…Several recent studies have shed new light on the mechanisms by which modifications in the tRNA core impact fitness and translation [ 110 , 111 , 132 ]. Effects of certain tRNA core modifications on fitness have been known for many years.…”