Mg²⁺ binding and archaeosine modification stabilize the G15–C48 Levitt base pair in tRNAs

Abstract

The G15-C48 Levitt base pair, located at a crucial position in the core of canonical tRNAs, assumes a reverse Watson-Crick (RWC) geometry. By means of bioinformatics analysis and quantum mechanics calculations we show here that such a geometry is moderately more stable than an alternative bifurcated trans geometry, involving the guanine Watson-Crick face and the cytosine keto group, which we have also found in known RNA structures. However we also demonstrate that the RWC geometry can take advantage of additional stabilizing effects such as metal binding or post-transcriptional chemical modification. One of the few strong metal binding sites characterized for cytosolic tRNAs is localized on G15, and a domain-specific complex modification known as archaeosine is widespread at position 15 in archaeal tRNAs. We have found that both the bound Mg 2+ ion and the archaeosine modification induce an analogous electron density redistribution, which results in an effective stabilization of the RWC geometry. Metal binding and chemical modification thus play an interchangeable role in stabilizing the G15-C48 correct geometry. Interestingly, these different but convergent strategies are selectively adopted in the different life domains.

Structural determinants for ligand capture by a class II preQ 1 riboswitch

“…The A-G base pair increases the C1′-C1′ distance by ∼1.5 Å, from 11.2 Å to 12.7 Å, and will have different stacking interactions (62), which may account for the differences in the C8-preQ 1 hydrogen bonds for the two riboswitches.…”

A Gateway platform for functional genomics in Haloferax volcanii: deletion of three tRNA modification genes

“…This modification is found at position 34 in five H. volcanii tRNAs (Gupta 1984, Gupta 1986), but its function is unknown. It has been postulated that the conformational rigidity of this nucleoside could stabilize RNA molecules of thermophilic archaea (Kawai et al 1992, Bruenger et al 1993, Oliva et al 2007). Our data indicate that an H. volcanii strain with tRNA lacking ac 4 C remains viable.…”

“…The function of archaeosine in vivo has yet to be investigated but its location has led to the hypothesis that it may function in stabilizing the tertiary structure of the tRNA through global interactions between the D-loop and the T-stem and loop (Gregson et al 1993). The archaeosine biosynthetic pathway is complex and poorly characterized (Oliva et al 2007). It has been shown that 7-cyano-7-deazaguanine (preQ 0 ) is an intermediate in the pathway and is inserted into tRNA by a tRNA-guanine transglycosylase (TGT, EC 2.4.2.29) encoded by the tgtA gene (Bai et al 2000, Watanabe et al 2001).…”

MD simulations of ligand-bound and ligand-free aptamer: Molecular level insights into the binding and switching mechanism of the add A-riboswitch

“…This observation, along with the fact that fluorescence experiments (Rieder et al 2007 (Ottink et al 2007) on the guanine-free G-riboswitch also indicate the importance of Mg 2+ ions in proper folding of the aptamer domain even in the absence of a ligand. It may be mentioned here, that Mg 2+ ions are known to stabilize even intrinsically unstable base-pairing geometries, as in the case of the Levitt base pair in tRNA (Oliva et al 2007).…”