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TRL1 tRNA ligase [ Saccharomyces cerevisiae S288C ]

Gene ID: 853358, updated on 2-Nov-2024

Summary

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Official Symbol
TRL1
Official Full Name
tRNA ligase
Primary source
SGD:S000003623
Locus tag
YJL087C
See related
AllianceGenome:SGD:S000003623; FungiDB:YJL087C; VEuPathDB:YJL087C
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Saccharomyces cerevisiae S288C (strain: S288C)
Lineage
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as
LIG1; RLG1
Summary
Enables 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity; GTP-dependent polyribonucleotide 5'-hydroxyl-kinase activity; and RNA ligase (ATP) activity. Involved in IRE1-mediated unfolded protein response; regulation of gene expression; and tRNA splicing, via endonucleolytic cleavage and ligation. Acts upstream of or within nuclear-transcribed mRNA catabolic process, no-go decay. Located in cytoplasm and nuclear inner membrane. [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See TRL1 in Genome Data Viewer
Location:
chromosome: X
Exon count:
1
Sequence:
Chromosome: X; NC_001142.9 (270002..272485, complement)

Chromosome X - NC_001142.9Genomic Context describing neighboring genes Neighboring gene Sip4p Neighboring gene ornithine carbamoyltransferase Neighboring gene GTP-Rho binding exocyst subunit EXO70 Neighboring gene Aly2p

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_001142.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Mechanism of action of a yeast RNA ligase in tRNA splicing. Greer CL, et al. Cell, 1983 Feb. PMID 6297798
  2. A fungal anticodon nuclease ribotoxin exploits a secondary cleavage site to evade tRNA repair. Meineke B, et al. RNA, 2012 Sep. PMID 22836353, Free PMC Article
  3. Structure-function analysis of yeast tRNA ligase. Wang LK, et al. RNA, 2005 Jun. PMID 15923379, Free PMC Article
  4. Characterization of polynucleotide kinase/phosphatase enzymes from Mycobacteriophages omega and Cjw1 and vibriophage KVP40. Zhu H, et al. J Biol Chem, 2004 Jun 18. PMID 15056675
  5. Multiple nucleotide cofactor use by yeast ligase in tRNA splicing. Evidence for independent ATP- and GTP-binding sites. Belford HG, et al. J Biol Chem, 1993 Feb 5. PMID 8428919

See all (60) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RNA kinase Trl1 is essential player in the degradation of No-Go Decay RNAs.
    Title: No-Go Decay mRNA cleavage in the ribosome exit tunnel produces 5'-OH ends phosphorylated by Trl1.
  2. Findings suggest for the tRNA ligase (Trl1) as an antifungal target.
    Title: Structural basis for the GTP specificity of the RNA kinase domain of fungal tRNA ligase.
  3. the mechanism for intron turnover requires healing of the 5' termini of linear introns by the tRNA ligase Rlg1 and destruction by the cytoplasmic tRNA quality control 5'-to-3' exonuclease Xrn1, which has specificity for RNAs with 5' monophosphate
    Title: Healing for destruction: tRNA intron degradation in yeast is a two-step cytoplasmic process catalyzed by tRNA ligase Rlg1 and 5'-to-3' exonuclease Xrn1.
  4. These results suggest that RNA ligase Trl1 for tRNA splicing might therefore commonly function as an RNA ligase for XBP1 mRNA splicing.
    Title: Function of yeast and amphioxus tRNA ligase in IRE1alpha-dependent XBP1 mRNA splicing.
  5. Structural requirements for the C-terminal 5'-kinase/2',3'-cyclic phosphodiesterase domain for Trl1 enzyme activity.
    Title: Structure-function analysis of the kinase-CPD domain of yeast tRNA ligase (Trl1) and requirements for complementation of tRNA splicing by a plant Trl1 homolog.
  6. Four essential residues Lys114, Glu184, Glu266, and Lys284 important for the structure and function of tRNA ligase were clarified.
    Title: Structure-function analysis of yeast tRNA ligase.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Gene Ontology Provided by SGD

Function Evidence Code Pubs
enables 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables GTP-dependent polyribonucleotide 5'-hydroxyl-kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables GTP-dependent polyribonucleotide 5'-hydroxyl-kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA ligase (ATP) activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA ligase (ATP) activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA ligase (ATP) activity IEA
Inferred from Electronic Annotation
more info
  
enables endonuclease activity IEA
Inferred from Electronic Annotation
more info
  
enables kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables ligase activity IEA
Inferred from Electronic Annotation
more info
  
enables phosphoric diester hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in IRE1-mediated unfolded protein response IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within nuclear-transcribed mRNA catabolic process, no-go decay IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in phosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of translation in response to stress IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in tRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in tRNA splicing, via endonucleolytic cleavage and ligation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tRNA splicing, via endonucleolytic cleavage and ligation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in tRNA splicing, via endonucleolytic cleavage and ligation IEA
Inferred from Electronic Annotation
more info
  
involved_in tRNA splicing, via endonucleolytic cleavage and ligation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear inner membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
tRNA ligase
NP_012448.1
  • 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; involved in turnover of tRNA introns; localized at the inner nuclear envelope and cytoplasm

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

  1. NC_001142.9 Reference assembly

    Range
    270002..272485 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001181520.1 → NP_012448.1  TPA: tRNA ligase [Saccharomyces cerevisiae S288C]

    See identical proteins and their annotated locations for NP_012448.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    D6VW97, P09880
    UniProtKB/TrEMBL
    B3LQ26, C7GR27, C8ZBC6, N1P8F7
    Conserved Domains (1) summary
    COG5324
    Location:1 → 827
    Trl1; tRNA splicing ligase [Translation, ribosomal structure and biogenesis]
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P09880.1

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