## 3 tRNA Core Modifications and Their Impact on Translation and Stress Adaptation
### tRNA Core Modifications and Their Impact on Translation and Fitness  
The binding of tRNAs to the ribosome and their accommodation into the A-site constitute the first steps of translation elongation. The reaction only becomes irreversible when fitting tRNAs enter the A-site [126], making accommodation a limiting step for translation elongation [126; 127]. Inside the A-site, tRNAs interact with the mRNA codon as well as the small ribosomal subunit via their anticodon-arm, leading to the well-characterized proofreading mechanism, and with the large ribosomal subunit mainly via their T-arm and elbow region [128; 129; 130; 11]. After the accommodation of the incoming tRNA into the A-site and the catalysis of the peptide transfer from the P- to the A-site tRNA, the peptidyl A-site tRNA is translocated to the P-site. During the translocation process, tRNAs also interact with the ribosome through their T-arm and elbow regions [129; 131; 132]. Modifications in the tRNA core that affect the structure and dynamics of tRNAs may therefore affect the interaction with the ribosome and modulate the efficiency of translation elongation by affecting accommodation and/or translocation. 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. For instance, in _E. coli_, the _trmA_ and _truB_ genes, responsible for the introduction of m\({}^{5}\)U54 and \(\Psi\)55 in the T-loop, are non-essential under most growth conditions, but subtle growth phenotypes have been reported for the _trmA_ and _truB_A strains [57; 133]. In addition, these genes are important for bacterial fitness in co-culture experiments [134; 135]. The fitness phenotypes in _E. coli_ are attributed to the chaperone activity of TruB [81], while both the chaperone and modification activities of TrmA are implicated [82]. The effect of m\({}^{5}\)U54 on translation was initially investigated in vitro with _E. coli_ tRNAs, which pointed towards a role for m\({}^{5}\)U54 in both translation speed and fidelity [136]. The binding to the A-site of a tRNA\({}^{\rm Lys(UUU)}\) lacking m\({}^{5}\)U54 was reduced, and the resulting translation speed increased by \(\sim\)10-fold, while translation with tRNA\({}^{\rm Phe(GAA)}\) displayed about a \(\sim\)10-fold loss of fidelity [136]. In yeast, there is a slight global increase in the translation efficiency in _trm2\(\Delta\)_ strains lacking m\({}^{5}\)U54 [137]. It is also worth mentioning that in humans, the m\({}^{5}\)U54 modification appears to be involved in translation fidelity [138]. In a recent report that conducted in vitro kinetic studies of translation with _E. coli_ tRNAs prepared from _trmA_\(\Delta\) cells, the m\({}^{5}\)U54 modification was shown to play a role in the translocation process [110]. The use of hygromycin B--an antibiotic known to block the translocation of ribosomes--led to the proposal that m\({}^{5}\)U54 affects the translocation step and could reduce the translation speed by restraining the translocation of tRNAs [110]. In another report that determined codon-specific changes in translation efficiency in the _trmA_\(\Delta\) and _truB_\(\Delta\) single- and double-knockout strains, a set of specific codons affecting the expression of a reporter gene was identified [111]. For instance, in the _truB_\(\Delta\) strain, a decrease in translation is detected when some arginine codons, i.e., CGU, CGG and AGG, are placed consecutively. Similarly, in the _trmA_\(\Delta\) strain, translation is decreased at consecutive cysteine TGT codons but increased at consecutive tyrosine TAT codons [111]. Although the overall translation is unaffected, the codon-specific impact related to the loss of m\({}^{5}\)U54 and/or \(\Psi\)55 in the \(trmA\Delta\) and \(truB\Delta\) strains leads to changes in the abundance of specific proteins, many of which are implicated in metabolism and gene expression [111].