Quality Control Pathways for Nucleus-Encoded Eukaryotic tRNA Biosynthesis and Subcellular Trafficking

Abstract

tRNAs perform an essential role in translating the genetic code. They are long-lived RNAs that are generated via numerous posttranscriptional steps. Eukaryotic cells have evolved numerous layers of quality control mechanisms to ensure that the tRNAs are appropriately structured, processed, and modified. We describe the known tRNA quality control processes that check tRNAs and correct or destroy aberrant tRNAs. These mechanisms employ two types of exonucleases, CCA end addition, tRNA nuclear aminoacylation, and tRNA subcellular traffic. We arrange these processes in order of the steps that occur from generation of precursor tRNAs by RNA polymerase (Pol) III transcription to end maturation and modification in the nucleus to splicing and additional modifications in the cytoplasm. Finally, we discuss the tRNA retrograde pathway, which allows tRNA reimport into the nucleus for degradation or repair.

FIG 1

Overlapping layers of nucleus-encoded tRNA control pathways. (A) Quality control pathways for tRNAs encoded by intron-lacking genes. (B) tRNA quality control pathways encoded by intron-containing genes. tRNAs are shown as the cloverleaf structure with color-coded circles. Purple circles depict transcribed leader and trailer sequences at the 5′ and 3′ ends, respectively. Blue circles depict the mature exons. Green circles depict the posttranscriptionally added CCA nucleotides. A black circle indicates a modification known to occur on initial pre-tRNA transcripts. Orange, brown, and open circles indicate various posttranscriptional modifications. Yellow circles in panel B depict intron sequences. The canonical tRNA biosynthesis pathway and subcellular traffic patterns are indicated with black arrows. Red dotted arrows indicate aberrant pre-tRNAs that are processed too slowly at 3′ ends and are targeted to nuclear exosome. The green dotted arrow in panel A indicates that aberrant pre-tRNA^Met missing m¹A₅₈ is targeted to a nuclear exosome. Blue dotted arrows indicate premature nuclear export that occurs before 5′ and 3′ processing. Aberrant transcripts are returned to the nucleus via constitutive retrograde nuclear import and are either processed or degraded. Magenta and purple dotted arrows indicate premature nuclear export before complete modification; hypomodified tRNAs are indicated by magenta or purple circles and arrows. Hypomodified tRNAs may return to the nucleus via retrograde import or may be destroyed by the cytoplasmic RTD exonuclease, Xrn1. Imported hypomodified tRNAs are repaired or degraded by the Rat1 nuclear RTD exonuclease. Hypomodified tRNAs and/or tRNAs with improper structure may be marked by Cca1 to generate CCACCA 3′ termini and then degraded by RTD nucleases.