Conservation of an intricate circuit for crucial modifications of the tRNA^Phe anticodon loop in eukaryotes

Abstract

Post-transcriptional tRNA modifications are critical for efficient and accurate translation, and have multiple different roles. Lack of modifications often leads to different biological consequences in different organisms, and in humans is frequently associated with neurological disorders. We investigate here the conservation of a unique circuitry for anticodon loop modification required for healthy growth in the yeast Saccharomyces cerevisiae. S. cerevisiae Trm7 interacts separately with Trm732 and Trm734 to 2 ′ -O-methylate three substrate tRNAs at anticodon loop residues C 32 and N 34 , and these modifications are required for efficient wybutosine formation at m 1 G 37 of tRNA Phe . Moreover, trm7Δ and trm732Δ trm734Δ mutants grow poorly due to lack of functional tRNA Phe . It is unknown if this circuitry is conserved and important for tRNA Phe modification in other eukaryotes, but a likely human TRM7 ortholog is implicated in nonsyndromic X-linked intellectual disability. We find that the distantly related yeast Schizosaccharomyces pombe has retained this circuitry for anticodon loop modification, that S. pombe trm7Δ and trm734Δ mutants have more severe phenotypes than the S. cerevisiae mutants, and that tRNA Phe is the major biological target. Furthermore, we provide evidence that Trm7 and Trm732 function is widely conserved throughout eukaryotes, since human FTSJ1 and THADA, respectively, complement growth defects of S. cerevisiae trm7Δ and trm732Δ trm734Δ mutants by modifying C 32 of tRNA Phe , each working with the corresponding S. cerevisiae partner protein. These results suggest widespread importance of 2 ′ -O-methylation of the tRNA anticodon loop, implicate tRNA Phe as the crucial substrate, and suggest that this modification circuitry is important for human neuronal development.

Lack of tRNA-i6A modification causes mitochondrial-like metabolic deficiency in S. pombe by limiting activity of cytosolic tRNATyr, not mito-tRNA

“…In some cases ectopic overexpression of tRNA can rescue phenotypes of anticodon modification enzyme-lacking yeast (Bauer et al 2012;Fernández-Vázquez et al 2013;Guy and Phizicky 2015 , partially rescued both phenotypes although more so for rapamycin than glycerol ( Fig. 2A-…”

Factors That Shape Eukaryotic tRNAomes: Processing, Modification and Anticodon–Codon Use

“…We highlight two recent cases that involve position 37 of different tRNAs, the yW37 and i 6 A 37 of tRNA Phe and tRNAs Ser , respectively and their interdependent modifications elsewhere in their anticodon stem loop (ASL) [133,134] (Figure 5C). Regarding the position 37 modifications of these tRNAs, while bacterial tRNAs Phe and other bacterial tRNAs that decode UNN codons contain i 6 A 37 , the tRNAs Phe in eukaryotes almost without exception contain the hypermodified G nucleotide, yW37.…”

Transfer RNA methyltransferases with a SpoU‐TrmD (SPOUT) fold and their modified nucleosides in tRNA

“…The site specificity of Trm7 is regulated by the existence of a partner subunit (Trm732 or Trm734) [115,116]. The Cm32 modification in yeast tRNA Phe is required for the formation of wybutosine at position 37 from m 1 G37 [115,117]. The human counterpart of Trm7 is FTSJ1, in which mutations cause nonsyndromic X-linked mental retardation [118,119,120].…”

“…In eukaryotes, the 2’- O -methylation of ribose at position 34 is produced by the Trm7-Trm734 complex [114,115,116,117]. Therefore, similar to TrmJ, TrmL might have potential as a target protein for drug design.…”