Variation of tRNA modifications with and without intron dependency

Abstract

tRNAs have recently gained attention for their novel regulatory roles in translation and for their diverse functions beyond translation. One of the most remarkable aspects of tRNA biogenesis is the incorporation of various chemical modifications, ranging from simple base or ribose methylation to more complex hypermodifications such as formation of queuosine and wybutosine. Some tRNAs are transcribed as intron-containing pre-tRNAs. While the majority of these modifications occur independently of introns, some are catalyzed in an intron-inhibitory manner, and in certain cases, they occur in an intron-dependent manner. This review focuses on pre-tRNA modification, including intron-containing pre-tRNA, in both intron-inhibitory and intron-dependent fashions. Any perturbations in the modification and processing of tRNAs may lead to a range of diseases and disorders, highlighting the importance of understanding these mechanisms in molecular biology and medicine.

Keywords: RNA modification; enzyme; intron; pre-tRNA; processing; tRNA.

FIGURE 1

tRNA structures and tRNA splicing pathways. (A) Secondary structure of intron-containing pre-tRNA: the acceptor stem and TΨC loop (blue), D-loop and anticodon loop (gray), variable loop (pink), anticodon (green), and intron (orange). The intermediate nucleotides between the acceptor stem and D-loop are yellow with grey circles. Nucleotide base pairing is represented by black lines, with the anticodon-intron (A–I) pair highlighted in red. The nucleotide numbers indicate the positions adjacent to the intron insertion sites (positions 37/38) and the locations of known tRNA intron-dependent modification positions, excluding the anticodon (positions 34–36). Black arrows indicate the canonical intron insertion site. (B) Secondary (left) and tertiary (right) structures of mature tRNA are shown with the same color codes and nucleotide numbers as in A. (C) Cleavage of the tRNA splice site (left) and two distinct tRNA ligation pathways: the 5′-phosphate pathway (upper right) and the 3′-phosphate pathway (lower right). The tRNA body is represented in black and the intron in orange. Proteins involved in each chemical reaction are also shown.

FIGURE 2

tRNA intron and modifications. (A) Chemical structures of the RNA modifications discussed in this review, created using MarvinSketch (ChemAxion Ltd.). (B) tRNA intron-dependent modification. In S. cerevisiae, pre-tRNA^Ile _UAU undergoes intron-dependent pseudouridylation (Ψ) at U34 and U36 by Pus1p in the nucleus. Subsequently, the modified pre-tRNA is exported to the cytoplasm for splicing near the mitochondria. In the intronless allele, on the other hand, pre-tRNA^Ile _UAU lacking an intron undergoes modification at position 34 by the Elp1-6p complex to convert ncm⁵U. (C) Schematic representation of non-canonical base editing of the intron in Trypanosoma brucei pre-tRNA^Tyr _GUA. The 11-nucleotide intron is shown in orange, and the GUA anticodon is depicted in white with a blue circle. Black arrows indicate the intron insertion sites. In the right panel, edited nucleotides are highlighted in black. Editing is essential for proper intron processing by the tRNA endonuclease (as shown in D). (D) In Trypanosoma brucei, the intron-containing pre-tRNA^Tyr _GUA with edited intron, as shown on the right side of C, is exported to the cytoplasm as the primary export substrate. After cytoplasmic splicing, the post-spliced pre-tRNA^Tyr _GUA undergoes intron-inhibitory modification with queuosine (Q) by Trypanosoma brucei tRNA-guanine transglycosylase (TbTGT).