## 2 Influence of tRNA Core Modification on tRNA Structure and Stability
### Interdependence Involving tRNA Core Modifications  
Although some modifications are incorporated into tRNAs independently, modification circuits have been identified in which the prior presence of one modification influences the occurrence and incorporation of subsequent modifications [3; 100; 101; 102]. Most of the well-characterized modification circuits concern modifications in the ACL region. Few examples involving tRNA core modifications have been reported, both in bacteria and yeast (Figure 3). The mechanisms underlying the altered efficiency of tRNA modification incorporation by initial modifications are not yet well understood, but it is reasonable to propose that alterations in the local structure and/or dynamics of the tRNA would affect the catalytic efficiency of the subsequent enzymes. These alterations could occur at all steps of the catalytic cycle of the modification enzymes, from substrate binding to substrate release. The first tRNA core modification circuits identified were those found in _T. thermophilus_ tRNA\({}^{\text{Phe}}\) (Figure 3a). They regulate modification levels overall in response to temperature changes (reviewed in [94]). Briefly, at elevated temperatures, the prior presence of m\({}^{7}\)G46 promotes the introduction of Gm18 and m\({}^{1}\)A58, which subsequently promotes the incorporation of m\({}^{5}\)S\({}^{2}\)U54 [95; 103], with m\({}^{1}\)A58 and m\({}^{5}\)S\({}^{2}\)U54 being essential for the growth of  
\begin{table}
\begin{tabular}{c c c c c c} \hline
**Organism** & **tRNA** & **Lacking Modifications** & **Conditions** & **Degradation Pathway** & **References** \\ \hline _S. cerevisiae_ & pre-tRNA\({}^{\text{Met}}_{1}\) & m\({}^{1}\)A58 & 36 \({}^{\circ}\)C & Nuclear surveillance & [19; 90] \\ \hline _S. cerevisiae_ & tRNA\({}^{\text{Met}}_{1}\) & m\({}^{1}\)A58 & 27 \({}^{\circ}\)C, 34 \({}^{\circ}\)C & RTD & [91] \\ \hline _S. pombe_ & tRNA\({}^{\text{Met}}_{1}\) & m\({}^{1}\)A58 & 30 \({}^{\circ}\)C, 38.5 \({}^{\circ}\)C & RTD & [91] \\ \hline _S. cerevisiae_ & tRNA\({}^{\text{Tyr}}\) & m\({}^{1}\)G9 & 30 \({}^{\circ}\)C, late log phase, and w/ or w/o SFU & Met22-dependent & Met22-dependent & Met22-dependent & Met22-dependent & Met22-dependent & Met22-dependent \\ \hline _S. cerevisiae_ & tRNA\({}^{\text{Val(AAC)}}\) & m\({}^{7}\)G46 and (m\({}^{5}\)C or \(\Psi\)13 or D47) \({}^{\star}\) & 37 \({}^{\circ}\)C & RTD & [18; 96] \\ \hline _S. cerevisiae_ & tRNA\({}^{\text{Ser(CGA,UGA)}}\) & Um44 and ac\({}^{\text{AC}}\)C12 \({}^{\star}\) & 36.5 \({}^{\circ}\)C & RTD & [96; 97] \\ \hline _S. cerevisiae_ & tRNA\({}^{\text{Ser(CGA,UGA)}}\) & m\({}^{2}_{2}\)G26 and m\({}^{5}\)C \({}^{\star}\) & 37 \({}^{\circ}\)C & RTD & [98] \\ \hline _S. cerevisiae_ & tRNA\({}^{\text{Val(AAC)}}\) & m\({}^{7}\)G46 & 37 \({}^{\circ}\)C after thiolutin \(\text{\text{\text{\text{\text{\text{\text{\text{\text{\text{\text{\text{\text{\text{ \texttexttext{ \texttexttexttexttext{  }}}}}}}}}}}}}}\) & RTD & [98] \\ \hline _S. cerevisiae_ & tRNA\({}^{\text{Ser(CGA,UGA)}}\) & ac\({}^{4}\)C12 & 37 \({}^{\circ}\)C & RTD & [98] \\ \hline _S. cerevisiae_ & tRNA\({}^{\text{Ser(CGA,UGA)}}\) & m\({}^{2}_{2}\)G26 & 37 \({}^{\circ}\)C & RTD & [98] \\ \hline _S. pombe_ & tRNA\({}^{\text{Tyr(GUA)}}\) and \({}^{\text{T}}\)G46 & 36.5 \({}^{\circ}\)C, 37.5 \({}^{\circ}\)C,several thermophiles at high temperatures [104; 105; 106]. In addition, m\({}^{7}\)G46 promotes the incorporation of m\({}^{1}\)G37 in the ACL [95]. However, at low temperatures, the prior presence of V55 inhibits the introduction of Gm18, m\({}^{1}\)A58 and m\({}^{5}\)s\({}^{2}\)U54, maintaining sufficient tRNA structural flexibility to survive at lower temperatures [107]. In addition, at low temperatures, m\({}^{5}\)U54 stimulates the introduction of m\({}^{1}\)A58 [108]. In the yeast _S. cerevisiae_, the time-resolved monitoring with NMR spectroscopy of the maturation of a tRNA\({}^{\text{Phe}}\) transcript in yeast cell extracts revealed the existence of dependencies between tRNA core modifications [69].