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    TRL1 tRNA ligase [ Saccharomyces cerevisiae S288C ]

    Gene ID: 853358, updated on 18-Sep-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. Located in cytoplasm and nuclear inner membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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. tRNA ligase structure reveals kinetic competition between non-conventional mRNA splicing and mRNA decay. Peschek J, et al. Elife, 2019 Jun 25. PMID 31237564, Free PMC Article
    2. Structural similarities and functional differences clarify evolutionary relationships between tRNA healing enzymes and the myelin enzyme CNPase. Muruganandam G, et al. BMC Biochem, 2017 May 16. PMID 28511668, Free PMC Article
    3. 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
    4. Structure-function analysis of yeast tRNA ligase. Wang LK, et al. RNA, 2005 Jun. PMID 15923379, Free PMC Article
    5. 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

    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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