Human tRNAs with inosine 34 are essential to efficiently translate eukarya-specific low-complexity proteins

Abstract

The modification of adenosine to inosine at the wobble position (I34) of tRNA anticodons is an abundant and essential feature of eukaryotic tRNAs. The expansion of inosine-containing tRNAs in eukaryotes followed the transformation of the homodimeric bacterial enzyme TadA, which generates I34 in tRNAArg and tRNALeu, into the heterodimeric eukaryotic enzyme ADAT, which modifies up to eight different tRNAs. The emergence of ADAT and its larger set of substrates, strongly influenced the tRNA composition and codon usage of eukaryotic genomes. However, the selective advantages that drove the expansion of I34-tRNAs remain unknown. Here we investigate the functional relevance of I34-tRNAs in human cells and show that a full complement of these tRNAs is necessary for the translation of low-complexity protein domains enriched in amino acids cognate for I34-tRNAs. The coding sequences for these domains require codons translated by I34-tRNAs, in detriment of synonymous codons that use other tRNAs. I34-tRNA-dependent low-complexity proteins are enriched in functional categories related to cell adhesion, and depletion in I34-tRNAs leads to cellular phenotypes consistent with these roles. We show that the distribution of these low-complexity proteins mirrors the distribution of I34-tRNAs in the phylogenetic tree.

Commonality and diversity in tRNA substrate recognition in t6A biogenesis by eukaryotic KEOPSs

“…tRNA Thr (UGU) was one of the best substrates for Sc KEOPS ( Supplementary Figure S3 ; Supplementary Table S5 ). In addition, tRNA Thr (UGU) harbors no other modification in the anticodon loop besides t 6 A37 and m 3 C32, which requires t 6 A37 as a prerequisite ( 33 , 40 ); however, in the anticodon loop, tRNA Thr (AGU) contains I34 ( 41 ), and tRNA Lys (UUU) contains mcm 5 s 2 U34 ( 42 ). Therefore, tRNA Thr (UGU) was selected for studying the recognition mechanism at the anticodon loop.…”

Position 34 of tRNA is a discriminative element for m5C38 modification by human DNMT2

“…The coding sequences of human ADAT2 and ADAT3 were initially amplified from the Hela cells cDNA, then inserted between the EcoRI /HindIII and NdeI/XhoI sites of the pRSFDuet-1 expression vector (Novagen) respectively, which results in ADAT2 with the DNA sequence encoding an His 6 tag at its N-terminus and ADAT3 with the DNA sequence encoding an S-tag at its C-terminus and were translated to ADAT2 and ADAT3, separately. In eukaryotes, the heterodimeric enzyme ADAT, including ADAT2 and ADAT3, catalyzes inosine modification at position 34 (I 34) in seven or eight different eukaryotic tRNAs ( 44 , 45 ). All the primers used for the construction of recombined vectors containing DNMT2 / Dnmt2 , ADAT2 and ADAT3 are listed in supplementary Table S1.…”

The Importance of the Epi-Transcriptome in Translation Fidelity

“…The chemical origin of the I 34 base-pairing effect is the replacement of the hydrogen-donating amino group in the C6 position by a hydrogen-accepting oxygen [ 44 ]. Inosine contributes to the extension of the genetic code [ 50 ].…”