TRL1/YJL087C Summary Help

Standard Name TRL1
Systematic Name YJL087C
Alias LIG1 , RLG1 1
Feature Type ORF, Verified
Description tRNA ligase; required for tRNA splicing and for both splicing and translation of HAC1 mRNA in the UPR; has phosphodiesterase, polynucleotide kinase, and ligase activities; localized at the inner nuclear envelope and partially to polysomes (2, 3, 4 and see Summary Paragraph)
Name Description tRNA Ligase
Chromosomal Location
ChrX:272485 to 270002 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Gene Ontology Annotations All TRL1 GO evidence and references
  View Computational GO annotations for TRL1
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 2 genes
Classical genetics
Large-scale survey
reduction of function
11 total interaction(s) for 11 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 3
  • Affinity Capture-RNA: 3

Genetic Interactions
  • Negative Genetic: 2
  • Positive Genetic: 2
  • Synthetic Lethality: 1

Expression Summary
Length (a.a.) 827
Molecular Weight (Da) 95,336
Isoelectric Point (pI) 7.76
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrX:272485 to 270002 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..2484 272485..270002 2011-02-03 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | E.C. | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000003623

TRL1 encodes tRNA ligase, which is essential for tRNA splicing (5, 6, 7). Trl1p has phosphodiesterase, polynucleotide kinase, and ligase activities; each activity resides in a different domain (2). In tRNA processing, an intron is removed from the tRNA transcript by the multisubunit tRNA splicing endonuclease (encoded by SEN2, SEN15, SEN34, and SEN54); the resulting half-molecules are joined by Trl1p (8, 7) and the splice junction 2'-phosphate is removed by the tRNA 2'-phosphotransferase encoded by TPT1 (reviewed in reference 9). Deletion of TRL1 is lethal; tRNA splicing intermediates accumulate in cells depleted of Trl1p or in trl1 temperature-sensitive mutants at the restrictive temperature (8). Trl1p is found at the inner nuclear membrane, although Trl1p is not an integral membrane protein (10, 3). Trl1p is also involved in splicing the mRNA encoding Hac1p, a transcription factor that activates the expression of genes induced by the unfolded protein response (11, 12). A tRNA ligase isolated from Candida albicans is 42% identical to Trl1p (1).

Last updated: 2008-09-03 Contact SGD

References cited on this page View Complete Literature Guide for TRL1
1) Baymiller J, et al.  (1994) Isolation and sequence of the t-RNA ligase-encoding gene of Candida albicans. Gene 142(1):129-34
2) Xu Q, et al.  (1990) Domain structure in yeast tRNA ligase. Biochemistry 29(26):6132-8
3) Clark MW and Abelson J  (1987) The subnuclear localization of tRNA ligase in yeast. J Cell Biol 105(4):1515-26
4) Mori T, et al.  (2010) Dual Functions of Yeast tRNA Ligase in the Unfolded Protein Response: Unconventional Cytoplasmic Splicing of HAC1 Pre-mRNA Is Not Sufficient to Release Translational Attenuation. Mol Biol Cell 21(21):3722-34
5) Phizicky EM, et al.  (1986) Saccharomyces cerevisiae tRNA ligase. Purification of the protein and isolation of the structural gene. J Biol Chem 261(6):2978-86
6) Westaway SK, et al.  (1988) Structure and function of the yeast tRNA ligase gene. J Biol Chem 263(7):3171-6
7) Abelson J, et al.  (1998) tRNA splicing. J Biol Chem 273(21):12685-8
8) Phizicky EM, et al.  (1992) Yeast tRNA ligase mutants are nonviable and accumulate tRNA splicing intermediates. J Biol Chem 267(7):4577-82
9) Calvin K and Li H  (2008) RNA-splicing endonuclease structure and function. Cell Mol Life Sci 65(7-8):1176-85
10) Greer CL  (1986) Assembly of a tRNA splicing complex: evidence for concerted excision and joining steps in splicing in vitro. Mol Cell Biol 6(2):635-44
11) Sidrauski C, et al.  (1996) tRNA ligase is required for regulated mRNA splicing in the unfolded protein response. Cell 87(3):405-13
12) Kaufman RJ  (1999) Stress signaling from the lumen of the endoplasmic reticulum: coordination of gene transcriptional and translational controls. Genes Dev 13(10):1211-33