Loss of both wobbleU34 modifications in mcm5s2U tRNAs impairs rRNA biosynthesis, growth, and development in Arabidopsis thaliana

In eukaryotic cells, the first anticodon uridine base of cytosolic tRNALys(UUU), tRNAGlu(UUC), and tRNAGln(UUG) (wobbleU₃₄) is post transcriptionally modified through adding a methoxycarbonylmethyl group and substituting a sulfur at the fifth and second carbons, respectively, to form 5-methoxycarbonylmethyl-2-thiouridine. The simultaneous deletion of these two wobbleU₃₄ modifications causes lethality in mice and flies. Here, we report that deletion of both wobbleU₃₄ modifications results in severe growth retardation and morphological abnormalities in <i>Arabidopsis thaliana</i>. The results of Ribo-seq and RNA-seq analyses indicate that the ribosome occupancy of many transcripts is substantially different in the <i>Arabidopsis</i> mutant lacking both wobbleU₃₄ modifications compared with the wild type. Gene Ontology analysis shows that genes with altered ribosome occupancy are categorized as having RNA-binding properties. Several pre-rRNA processing precursors accumulate in the mutant lacking both wobbleU₃₄ modifications. In the mutant, ribosomes likely pause when the cognate [A/G/C]AA codons of tRNALys(UUU), tRNAGlu(UUC), and tRNAGln(UUG) are positioned at the A site during translation of transcripts encoding proteins involved in pre-rRNA processing, such as <i>DRH1</i> and <i>ATRH7</i>. These findings suggest that deleting both wobble U₃₄ modifications impairs rRNA maturation, leading to the accumulation of rRNA precursors adversely affecting growth and morphogenesis in plants.