The role of intracellular compartmentalization on tRNA processing and modification

Abstract

A signature of most eukaryotic cells is the presence of intricate membrane systems. Intracellular organization presumably evolved to provide order, and add layers for regulation of intracellular processes; compartmentalization also forcibly led to the appearance of sophisticated transport systems. With nucleus-encoded tRNAs, it led to the uncoupling of tRNA synthesis from many of the maturation steps it undergoes. It is now clear that tRNAs are actively transported across intracellular membranes and at any point, in any compartment, they can be post-transcriptionally modified; modification enzymes themselves may localize to any of the genome-containing compartments. In the following pages, we describe a number of well-known examples of how intracellular compartmentalization of tRNA processing and modification activities impact the function and fate of tRNAs. We raise the possibility that rates of intracellular transport may influence the level of modification and as such increase the diversity of differentially modified tRNAs in cells.

Keywords: Maturation; modification; nuclear export; retrograde transport; tRNA splicing.

Figure 1.

Tertiary contacts critical for global tRNA structure. A General tRNA cloverleaf structure highlighting the numbering scheme and important tertiary contacts between tRNA arms shown as dashed lines. Darker circles represent nucleotides, which when altered, disrupts the stability and export of the tRNA. Many nucleotide contacts that disrupt export are also those involved in inter-arm base pairing between the D and TΨC arms. B As tRNA tertiary structure is disrupted, certain modifications will be negatively affected while others may not. In blue are positions in which corresponding modification enzymes can tolerate global tertiary structural changes while those shown in red do not tolerate tertiary alteration of the tRNA.

Figure 2.

Two major surveillance pathways for defective tRNAs. A. tRNA_i^Met lacking m¹A₅₈ is polyadenylated by the TRAMP complex (Trf4/5, Air1/2). The helicase Mtr4 assists the TRAMP complex and targets TRAMP to the nuclear endonuclease complex consisting of several structural proteins and a 3’ to 5’ exonuclease. B. The rapid tRNA decay pathway (RTD) degrades hypomodified tRNA^Val and tRNA^Ser.

Figure 3.

Several modifications depend on the presence of an intron in tRNA. A Certain modifications (as indicated) can only be added to intron-containing tRNA; the intron is an essential recognition element for their respective enzyme. B Some modifications are only added after splicing (as indicated).

Figure 4.

The biosynthesis of wybutosine (yW) in S. cereviase requires retrograde transport of tRNA^Phe to the nucleus. Intron-containing tRNA^Phe is exported to the cytoplasm from the nucleus, where the intron is cleaved by the heterotetrameric splicing endonuclease, which localizes to the outer surface of the mitochondria facing the cytoplasm endonuclease. The exons are then processed by the tRNA-splicing ligase (Trl1) and the tRNA phosphotransferase (Tpt1) to complete the splicing reaction. The newly spliced tRNA^Phe is imported back into the nucleus (retrograde transport) where a nucleus-localized 1-methyltransferase Trm5 forms m¹G₃₇. The methylated tRNA is then re-exported to the cytoplasm, where a series of reactions catalyzed by Tyw1, Tyw2, Tyw3, Tyw4 ultimately creates yW₃₇.

Figure 5.

The biosynthesis of queuosine (Q) in T. brucei requires retrograde transport of tRNA^Tyr to the nucleus. The only intron-containing tRNA in T. brucei, tRNA^Tyr, is exported to the cytoplasm for splicing by the tRNA splicing-specific endonuclease, ligase (Trl1) and phosphotransferase (Tpt1). After splicing tRNA^Tyr travels back to the nucleus where the nucleus-localized tRNA guanosyl transglycosylase (TGT) forms Q₃₄.

Figure 6.

The connection between tRNA thiolation and mitochondrial import in L. tarentolae and T. brucei. A. Thiolation of tRNA^Glu andtRNA^Gln acts as a negative determinant of mitochondrial import in L. tarentolae, but not in T. brucei. B. A portion of tRNA^Trp is kept for cytoplasmic translation, while another is imported into the mitochondria. In the mitochondrial lumen, tRNA^Trp is subjected to thiolation at the unusual position U₃₃ and edited from C to U at position 34. In L. tarentolae, only the edited tRNA gets thiolated whilst in T. brucei, thiolation acts as a negative determinant for editing. The same enzyme Nisf1, is responsible for thiolation of cytoplasmic tRNA^Glu andtRNA^Gln at position U₃₄.