RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics

Abstract

A plethora of modified nucleotides extends the chemical and conformational space for natural occurring RNAs. tRNAs constitute the class of RNAs with the highest modification rate. The extensive modification modulates their overall stability, the fidelity and efficiency of translation. However, the impact of nucleotide modifications on the local structural dynamics is not well characterized. Here we show that the incorporation of the modified nucleotides in tRNAfMet from Escherichia coli leads to an increase in the local conformational dynamics, ultimately resulting in the stabilization of the overall tertiary structure. Through analysis of the local dynamics by NMR spectroscopic methods we find that, although the overall thermal stability of the tRNA is higher for the modified molecule, the conformational fluctuations on the local level are increased in comparison to an unmodified tRNA. In consequence, the melting of individual base pairs in the unmodified tRNA is determined by high entropic penalties compared to the modified. Further, we find that the modifications lead to a stabilization of long-range interactions harmonizing the stability of the tRNA’s secondary and tertiary structure. Our results demonstrate that the increase in chemical space through introduction of modifications enables the population of otherwise inaccessible conformational substates.

Current Status of Epitranscriptomic Marks Affecting lncRNA Structures and Functions

“…As it is evident that lncRNAs are modified by various epitranscriptomic enzymes, it is still difficult to understand what these epitranscriptomic marks mean for the functions of lncRNAs with largely unknown functions. Furthermore, a recent study about epitranscriptomic marks on tRNAs show that epitranscriptomic marks affect tertiary structures of tRNAs [142], suggesting that not only secondary structures but also tertiary structures of lncRNAs must be carefully analyzed for the presence of epitranscriptomic marks on lncRNAs. Given that sequence information alone cannot infer the functions of lncRNAs, careful inspections of secondary and tertiary structures of lncRNAs are necessary to uncover the functions of lncRNAs as their mechanisms of actions depend on their bindings to macromolecules.…”

Different modification pathways for m1A58 incorporation in yeast elongator and initiator tRNAs

“…The comparison of the NMR spectra of Ψ55- and T54-containing tRNA Phe with that of the unmodified tRNA Phe , showing very limited chemical shift variations, suggests that these modifications do not induce large global rearrangements in the structure of tRNA Phe (38,45). The effect of the modifications on the efficiency of the downstream enzymes is therefore most likely related to local and/or global changes in the dynamic properties of the tRNA substrate, as recently reported in the case of E. col i tRNAfMet, in which conformational fluctuations on the local level are increased in the modified tRNA (63). Modifications could thus help reach otherwise inaccessible structural conformations that are more suited to the subsequent modification enzyme.…”

tRNA Modifications and Modifying Enzymes in Disease, the Potential Therapeutic Targets

“…Therefore, modified nucleotides affect the folding and structure of tRNA in a variety of ways, which is conducive to the construction of the most efficient ASL conformation for effective translation. It is worth noting that although some modifications do not affect the overall structure, they can modulate local dynamics, make tRNA's secondary and tertiary structure harmonized [42].…”