tRNA Structural Stability and Functionality Associated with the RNA Chaperone La and Post-Transcriptional Modification Enzyme Trm1

RNA molecules have a high propensity in becoming kinetically trapped in misfolded, inactive conformations that have similar thermodynamic stability as the native fold. To ensure native folding and biological activity, RNA species undergo PTMs while concomitantly associating with RNA-binding proteins. tRNAs are essential noncoding RNAs that are ubiquitously subject to PTMs and in constant interactions with various RNA-binding proteins. La proteins are a class of highly abundant RNA chaperones, characterized as the initial factors that contact pre-tRNAs. La proteins make sequence specific contacts to the UUU-3OH ends of pre-tRNAs as well as less specific contacts to the core body of tRNAs which is associated with the RNA chaperone activity function. La proteins function redundantly with tRNA PTM enzymes that are predicted to be influential in native pre-tRNA folding and N2, N2-dimethylation of G26 by the methyltransferase Trm1p is an example of such modification enzyme. La deletion in Saccharomyces cerevisiae (S. cerevisiae) is synthetically lethal when combined with deletion of Trm1p, presumably due to numerous G26 containing pre-tRNAs undergoing degradation due to structural instability. Whether La as an RNA chaperone selectively identifies such misfolded pre-tRNAs from their folded counterparts has not been addressed. In this work, we demonstrate that like S. cerevisiae, La and Trm1p are essential for viability in Schizosaccharomyces pombe (S. pombe). We have identified G26 containing pre-tRNAs that benefit from the presence of Trm1p and/or S. pombe La for their native steady state abundance and charging state. Using in vivo and in vitro assays we test the affinity of La as an RNA chaperone towards misfolded Trm1p-hypomodified pre-tRNAs and their folded Trm1p-modified counterparts. Our data indicates a nonspecific and transient nature of La in engaging misfolded and folded pre-tRNAs indiscriminately but specifically as processing intermediates. These findings signify the challenges that exist for RNA chaperones in resolving misfolded RNA structures with the inability to directly specify a binding determinant in these misfolded species. We also demonstrate that m22G26 on both mitochondrial and nuclear encoded-tRNAs may play a regulatory role on tRNA functional activity in translation, with the potential to directly regulate global protein expression levels and mitochondrial fitness.