Role of a tRNA Base Modification and Its Precursors in Frameshifting in Eukaryotes

Abstract

Little is known about the role of specific base modifications of transfer RNAs. Wyosine bases are tRNA(Phe)-specific modifications that are distinguished by differentiated, lateral side chains and base methylations appended to the core ring structure of a universally conserved G37, adjacent to the anticodon of Phe tRNAs. Based on previous data, we hypothesized that this modification was needed for -1 frameshifting. Using a reporter system incorporating a SCV-LA yeast virus slippery site for detecting -1 frameshifts in vivo, yeast strains were created that enabled chemical-genetic dissection of the role of different functional groups of wyebutosine that are added in a three-step post-transcriptional set of reactions. With this system, hypomodification increased Phe-specific frameshifting, with incremental changes in frameshift efficiency after specific intermediates in the progression of wyebutosine synthesis. These data combined with investigations of wild-type and hypomodified tRNA binding to ribosomes suggest that frameshift efficiency is kinetically and not thermodynamically controlled. The progressive nature of frameshift efficiency with the stage of modification is consistent with a stepwise evolution and tuning of frameshift potential. The stepwise tuning of frameshift efficiency could explain why tRNA(Phe) in some eukaryotes is not fully modified but, rather, hypomodified to capture a specific frameshift potential.

Overexpression of initiator methionine tRNA leads to global reprogramming of tRNA expression and increased proliferation in human epithelial cells

“…However, the question remains whether they are truly fully functional in the cell. In vitro transcribed tRNAs lack the post-transcriptional modifications characteristic of endogenous tRNAs that serve as identity determinants, contribute to tRNA stability, and impact translational accuracy (Alexandrov et al 2006;Agris et al 2007;Waas et al 2007;Phizicky and Hopper 2010). This is particularly relevant for our tRNA of interest: tRNA i…”

Transfer RNA Post-Transcriptional Processing, Turnover, and Subcellular Dynamics in the YeastSaccharomyces cerevisiae

“…Modifications in the anticodon loop can also affect the reading frames during translation. For example, mutations of the genes responsible for (yW) modification of tRNA Phe at position 37 cause increases in 21 frameshifting (Waas et al 2007).…”

Protein folding and tRNA biology

“…In regard to tRNA modifications, their functions include: stability and flexibility of the tRNA structure (Motorin and Helm 2010), translational fidelity via codon-anticodon interaction (Saint-Léger and Ribas de Pouplana 2015), reading frame maintenance (Waas et al 2007;Delaunay et al 2016;Klassen et al 2016a), tRNA discrimination , nonsense suppression (Benko et al 2000), tRNA stability (Alexandrov et al 2006;Kotelawala et al 2008;Dewe et al 2012), proteome integrity (Nedialkova and Leidel 2015), sensitivity to aminoglycoside antibiotics acting at the decoding site of ribosomes (Kalhor and Clarke 2003), response to stress (Kamenski et al 2007;Chan et al 2012;Gu et al 2014), and recognition of tRNA as either self or nonself by TLR7 receptor (Kaiser et al 2014;Rimbach et al 2015). For general reviews, see Helm (2011), Hopper (2013) and Phizicky and Hopper (2015).…”