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    XRN4 exoribonuclease 4 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 841891, updated on 18-Sep-2024

    Summary

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    Official Symbol
    XRN4
    Official Full Name
    exoribonuclease 4
    Primary source
    TAIR:AT1G54490
    Locus tag
    AT1G54490
    See related
    Araport:AT1G54490
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    5'-3' EXORIBONUCLEASE; ACC INSENSITIVE 1; AIN1; ATXRN4; EIN5; ETHYLENE INSENSITIVE 5; exoribonuclease 4; EXORIBONUCLEASE 4; F20D21.30; F20D21_30
    Summary
    Involved in the ethylene response. XRN4 does not appear to regulate ethylene signaling via an RNA-INDUCED SILENCING COMPLEX-based RNA silencing mechanism but acts by independent means. Endogenous suppressor of posttranscriptional gene silencing.
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    Genomic context

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    See XRN4 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    22
    Sequence:
    Chromosome: 1; NC_003070.9 (20350109..20356916)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene resistance to peronospora parasitica protein Neighboring gene LRR receptor-like Serine/Threonine-kinase Neighboring gene Rubredoxin-like superfamily protein Neighboring gene NIMA-related serine/threonine kinase 1

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003070.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. The second face of a known player: Arabidopsis silencing suppressor AtXRN4 acts organ-specifically. Vogel F, et al. New Phytol, 2011 Jan. PMID 21039560
    2. Ethylene can stimulate Arabidopsis hypocotyl elongation in the light. Smalle J, et al. Proc Natl Acad Sci U S A, 1997 Mar 18. PMID 11038610, Free PMC Article
    3. A link between mRNA turnover and RNA interference in Arabidopsis. Gazzani S, et al. Science, 2004 Nov 5. PMID 15528448
    4. Expression of the Arabidopsis Xrn4p 5'-3' exoribonuclease facilitates degradation of tombusvirus RNA and promotes rapid emergence of viral variants in plants. Cheng CP, et al. Virology, 2007 Nov 25. PMID 17688902
    5. Loss of XRN4 function can trigger cosuppression in a sequence-dependent manner. Hayashi M, et al. Plant Cell Physiol, 2012 Jul. PMID 22611176

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Beyond demonstrating that XRN4 is a major player in multiple decay pathways, this study identified intriguing molecular impacts of the enzyme, including those that led to new insights about mRNA decay and discovery of functional contributions at the whole-plant level
      Title: RNA degradomes reveal substrates and importance for dark and nitrogen stress responses of Arabidopsis XRN4.
    2. Data suggest that specific motifs, secondary energy, and GC content of transcripts could play a role in their degradation by exoribonuclease4 (xrn4) and varicose (vcs).
      Title: 5' to 3' mRNA Decay Contributes to the Regulation of Arabidopsis Seed Germination by Dormancy.
    3. These results demonstrate that AtXRN4-mediated mRNA degradation is linked to the suppression of heat acclimation.
      Title: Loss of Arabidopsis 5'-3' Exoribonuclease AtXRN4 Function Enhances Heat Stress Tolerance of Plants Subjected to Severe Heat Stress.
    4. XRN4 is required to set up a massive heat-induced mRNA decay.
      Title: XRN4 and LARP1 are required for a heat-triggered mRNA decay pathway involved in plant acclimation and survival during thermal stress.
    5. Loss of XRN4 function can potentially trigger the cosuppression in a sequence-dependent manner.
      Title: Loss of XRN4 function can trigger cosuppression in a sequence-dependent manner.
    6. Map based cloning identified in both lines mutations in XRN4 (Exoribonuclease 4), which was previously described as a suppressor of transgene silencing in source leaves.
      Title: The second face of a known player: Arabidopsis silencing suppressor AtXRN4 acts organ-specifically.
    7. RNA silencing modulated by FRY1 and XRN4 plays an important role in shaping root architecture.
      Title: The bifunctional abiotic stress signalling regulator and endogenous RNA silencing suppressor FIERY1 is required for lateral root formation.
    8. Xrn1p is involved in TBSV RNA degradation affecting recombination.
      Title: Expression of the Arabidopsis Xrn4p 5'-3' exoribonuclease facilitates degradation of tombusvirus RNA and promotes rapid emergence of viral variants in plants.
    9. The identification of XRN4 as an integral new component in ethylene signaling adds RNA degradation as another posttranscriptional process that modulates the perception of this plant hormone.
      Title: The exoribonuclease XRN4 is a component of the ethylene response pathway in Arabidopsis.
    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

    NM_001333652.1
    NM_104327.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables 5'-3' RNA exonuclease activity IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    enables 5'-3' RNA exonuclease activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables mRNA binding HDA PubMed 
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cell division IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within cellular heat acclimation IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within cellular heat acclimation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within deadenylation-independent decapping of nuclear-transcribed mRNA IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within epigenetic regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within ethylene-activated signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within ethylene-activated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		  
    acts_upstream_of_or_within gravitropism IMP
    Inferred from Mutant Phenotype
    more info
    		  
    involved_in heat acclimation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mRNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within miRNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within nuclear-transcribed mRNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within phloem or xylem histogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of mRNA catabolic process IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within response to 1-aminocyclopropane-1-carboxylic acid IMP
    Inferred from Mutant Phenotype
    more info
    		  
    acts_upstream_of_or_within response to ethylene IMP
    Inferred from Mutant Phenotype
    more info
    		  
    acts_upstream_of_or_within unidimensional cell growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in P-body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasmic stress granule IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    exoribonuclease 4
    NP_175851.1
    • exoribonuclease 4 (XRN4); CONTAINS InterPro DOMAIN/s: 5'-3' exoribonuclease 2 (InterPro:IPR017151), Zinc finger, CCHC-type (InterPro:IPR001878), Putative 5-3 exonuclease (InterPro:IPR004859); BEST Arabidopsis thaliana protein match is: 5'-3' exoribonuclease 3 (TAIR:AT1G75660.1); Has 1935 Blast hits to 1539 proteins in 314 species: Archae - 0; Bacteria - 132; Metazoa - 355; Fungi - 561; Plants - 185; Viruses - 14; Other Eukaryotes - 688 (source: NCBI BLink).

    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_003070.9 Reference assembly

      Range
      20350109..20356916
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_104327.4 → NP_175851.1  exoribonuclease 4 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_175851.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9FQ04, Q9SLI5
      UniProtKB/TrEMBL
      A0A178WFK9, A0A384KRW9, Q17Q78
      Conserved Domains (1) summary
      COG5049
      Location:1 → 849
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]

    2. NM_001333652.1 → NP_001321327.1  exoribonuclease 4 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8AQR8
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9FQ04.1

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