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protein coding gene - dhp1 (SPAC26A3.12c) - 5'-3' exoribonuclease Dhp1

Gene summary

Standard name
dhp1
Systematic ID
SPAC26A3.12c
Product
5'-3' exoribonuclease Dhp1
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
rat1
UniProt ID
P40848
ORFeome ID
29/29G08
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome I: 3356144..3361003 reverse strand

Annotation

Complementation

PBO:0016059 - functionally complements S. cerevisiae RAT1

References:

PBO:0016060 - functionally complements S. cerevisiae XRN1

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PBO:0123297 - is not functionally complemented by S. cerevisiae XRN1

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GO biological process

GO:0000448 - cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

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GO:0071028 - nuclear mRNA surveillance

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GO:0000956 - nuclear-transcribed mRNA catabolic process

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GO:0180037 - rapid tRNA decay

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GO cellular component

GO:0090730 - Las1 complex

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GO:0005634 - nucleus

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GO molecular function

GO:0004534 - 5'-3' RNA exonuclease activity

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GO:0005515 - protein binding

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GO:0003723 - RNA binding

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Modification

MOD:00046 - O-phospho-L-serine

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MOD:00047 - O-phospho-L-threonine

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MOD:00048 - O4'-phospho-L-tyrosine

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Multi-locus phenotype

FYPO:0008415 - abnormal centromeric outer repeat transcript localization to the cytoplasm

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Genotypes:

FYPO:0000082 - decreased cell population growth at high temperature

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Genotypes:

FYPO:0001407 - decreased cell population growth on glucose carbon source

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Genotypes:

FYPO:0002583 - decreased mature tRNA level during vegetative growth

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Genotypes:

FYPO:0000220 - increased centromeric outer repeat transcript level

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Genotypes:

FYPO:0002061 - inviable vegetative cell population

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Genotypes:

FYPO:0000674 - normal cell population growth at high temperature

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Genotypes:

FYPO:0003153 - normal protein level during cellular response to heat

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Genotypes:

FYPO:0001986 - resistance to 5-fluorouracil

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Genotypes:

Qualitative gene expression

PomGeneEx:0000019 - protein level decreased

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PomGeneEx:0000014 - RNA present

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Quantitative gene expression

PBO:0006310 - protein level

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PBO:0011963 - RNA level

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Single locus phenotype

FYPO:0000608 - abnormal cell cycle arrest in mitotic M phase

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Genotypes:

FYPO:0001679 - abnormal protein localization to chromatin

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Genotypes:

FYPO:0004811 - abnormal termination of RNA polymerase II transcription

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Genotypes:

FYPO:0003556 - abnormal transcription termination

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Genotypes:

FYPO:0000705 - abolished protein-protein interaction

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Genotypes:

FYPO:0001270 - complete but unequal mitotic sister chromatid segregation

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Genotypes:

FYPO:0000082 - decreased cell population growth at high temperature

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Genotypes:

FYPO:0004604 - decreased chromatin silencing at subtelomere

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Genotypes:

FYPO:0007883 - decreased cleavage-dependent termination of RNA polymerase II transcription

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Genotypes:

FYPO:0007223 - decreased establishment of chromatin silencing at centromere outer repeat region

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Genotypes:

FYPO:0003151 - decreased protein level during cellular response to heat

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Genotypes:

FYPO:0006613 - decreased termination of RNA polymerase II transcription

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Genotypes:

FYPO:0003119 - increased nuclear polyadenylated mRNA level during vegetative growth

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Genotypes:

FYPO:0003700 - increased snoRNA primary transcript level

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Genotypes:

FYPO:0001991 - inviable after spore germination, without cell division

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Genotypes:

FYPO:0002303 - inviable mononucleate monoseptate vegetative cell with anucleate compartment

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Genotypes:

FYPO:0002151 - inviable spore

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Genotypes:

FYPO:0002061 - inviable vegetative cell population

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Genotypes:

FYPO:0006518 - loss of viability in G0

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Genotypes:

FYPO:0001164 - normal growth on glucose carbon source

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Genotypes:

FYPO:0000488 - normal meiotic recombination

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Genotypes:

FYPO:0004093 - normal meiotic telomere clustering

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Genotypes:

FYPO:0000703 - normal protein-protein interaction

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Genotypes:

FYPO:0002687 - normal telomere length during vegetative growth

References:

Genotypes:

Taxonomic conservation

PBO:0011065 - conserved in eukaryotes

PBO:0011071 - conserved in eukaryotes only

PBO:0011064 - conserved in fungi

PBO:0011069 - conserved in metazoa

PBO:0011070 - conserved in vertebrates

PBO:0006222 - predominantly single copy (one to one)

Protein features

IDNameInterPro nameDB name
PF03159XRN_NXrn1_NPfam
PF17846XRN_MXrn1_helicalPfam
cd18673PIN_XRN1-2-likeCDD
G3DSA:1.25.40.1050:FF:000002CATH-FunFam
G3DSA:3.40.50.12390:FF:000003CATH-FunFam
G3DSA:3.40.50.12390:FF:000005CATH-FunFam
G3DSA:1.25.40.1050CATH-Gene3D
G3DSA:3.40.50.12390CATH-Gene3D
PTHR123415_3_exoribonucleasePANTHER
PIRSF037239Exonuclease_Xrn2Xrn2/3/4PIRSF
CoilCOILS
mobidb-lite-Disorderdisorder_predictionMobiDB-Disorder
mobidb-lite-Glycine-richdisorder_predictionMobiDB-Glycine-rich
mobidb-lite-Low-complexitydisorder_predictionMobiDB-Low-complexity
mobidb-lite-Polardisorder_predictionMobiDB-Polar
mobidb-lite-Polyampholytedisorder_predictionMobiDB-Polyampholyte

Orthologs

References / Literature

PMID:19366728 - Genetic control of cellular quiescence in S. pombe.
Sajiki K et al. J Cell Sci 2009 May 01;122(Pt 9):1418-29
PMID:28031482 - Involvement of fission yeast Pdc2 in RNA degradation and P-body function.
Wang CY et al. RNA 2017 Apr;23(4):493-503
PMID:30726745 - Fission Yeast NDR/LATS Kinase Orb6 Regulates Exocytosis via Phosphorylation of the Exocyst Complex.
Tay YD et al. Cell Rep 2019 Feb 05;26(6):1654-1667.e7
PMID:39367033 - Quantitative proteomics and phosphoproteomics profiling of meiotic divisions in the fission yeast Schizosaccharomyces pombe.
Sivakova B et al. Sci Rep 2024 Oct 04;14(1):23105
PMID:26889830 - A Novel Epigenetic Silencing Pathway Involving the Highly Conserved 5'-3' Exoribonuclease Dhp1/Rat1/Xrn2 in Schizosaccharomyces pombe.
Tucker JF et al. PLoS Genet 2016 Feb;12(2):e1005873
PMID:24763107 - Absolute proteome and phosphoproteome dynamics during the cell cycle of Schizosaccharomyces pombe (Fission Yeast).
Carpy A et al. Mol Cell Proteomics 2014 Aug;13(8):1925-36
PMID:11238999 - The dhp1(+) gene, encoding a putative nuclear 5'-->3' exoribonuclease, is required for proper chromosome segregation in fission yeast.
Shobuike T et al. Nucleic Acids Res 2001 Mar 15;29(6):1326-33
PMID:20609363 - Pac1 endonuclease and Dhp1p 5'-->3' exonuclease are required for U3 snoRNA termination in Schizosaccharomyces pombe.
Nabavi S et al. FEBS Lett 2010 Aug 04;584(15):3436-41
PMID:31615333 - Condensin locates at transcriptional termination sites in mitosis, possibly releasing mitotic transcripts.
Nakazawa N et al. Open Biol 2019 Oct 31;9(10):190125
PMID:23697806 - A genome-wide resource of cell cycle and cell shape genes of fission yeast.
Hayles J et al. Open Biol 2013 May 22;3(5):130053
PMID:20152800 - Cleavage-induced termination in U2 snRNA gene expression.
Nabavi S et al. Biochem Biophys Res Commun 2010 Mar 12;393(3):461-5
PMID:24713849 - Post-transcriptional regulation of meiotic genes by a nuclear RNA silencing complex.
Egan ED et al. RNA 2014 Jun;20(6):867-81
PMID:10409438 - Cloning and mapping of the XRN2 gene to human chromosome 20p11.1-p11.2.
Zhang M et al. Genomics 1999 Jul 15;59(2):252-4
PMID:20473289 - Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.
Kim DU et al. Nat Biotechnol 2010 Jun;28(6):617-623
PMID:22912768 - Rhn1, a nuclear protein, is required for suppression of meiotic mRNAs in mitotically dividing fission yeast.
Sugiyama T et al. PLoS One 2012;7(8):e42962
PMID:35901126 - Initiator tRNA lacking 1-methyladenosine is targeted by the rapid tRNA decay pathway in evolutionarily distant yeast species.
Tasak M et al. PLoS Genet 2022 Jul;18(7):e1010215
PMID:24013502 - Epe1 recruits BET family bromodomain protein Bdf2 to establish heterochromatin boundaries.
Wang J et al. Genes Dev 2013 Sep 01;27(17):1886-902
PMID:33823663 - A TOR (target of rapamycin) and nutritional phosphoproteome of fission yeast reveals novel targets in networks conserved in humans.
Halova L et al. Open Biol 2021 Apr;11(4):200405
GO_REF:0000024 - Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity.
PMID:34352089 - Co-transcriptional RNA cleavage by Drosha homolog Pac1 triggers transcription termination in fission yeast.
Yague-Sanz C et al. Nucleic Acids Res 2021 Sep 07;49(15):8610-8624
PMID:27401558 - The Nrd1-like protein Seb1 coordinates cotranscriptional 3' end processing and polyadenylation site selection.
Lemay JF et al. Genes Dev 2016 Jul 01;30(13):1558-72
PMID:25720772 - Quantitative phosphoproteomics reveals pathways for coordination of cell growth and division by the conserved fission yeast kinase pom1.
Kettenbach AN et al. Mol Cell Proteomics 2015 May;14(5):1275-87
GO_REF:0000111 - Gene Ontology annotations Inferred by Curator (IC) using at least one Inferred by Sequence Similarity (ISS) annotation to support the inference
PMID:40185772 - A bifunctional snoRNA with separable activities in guiding rRNA 2'-O-methylation and scaffolding gametogenesis effectors.
Leroy E et al. Nat Commun 2025 Apr 05;16(1):3250
PMID:40063661 - Fission yeast Caprin protein is required for efficient heterochromatin establishment.
Zhang H et al. PLoS Genet 2025 Mar 10;21(3):e1011620
PMID:30355493 - Expanded Interactome of the Intrinsically Disordered Protein Dss1.
Schenstrøm SM et al. Cell Rep 2018 Oct 23;25(4):862-870
PMID:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
PMID:24818994 - The S. pombe translation initiation factor eIF4G is Sumoylated and associates with the SUMO protease Ulp2.
Jongjitwimol J et al. PLoS One 2014;9(5):e94182
PMID:38295128 - A connection between the ribosome and two S. pombe tRNA modification mutants subject to rapid tRNA decay.
De Zoysa T et al. PLoS Genet 2024 Jan 31;20(1):e1011146
PMID:9572142 - Defective meiosis in telomere-silencing mutants of Schizosaccharomyces pombe.
Nimmo ER et al. Nature 1998 Apr 23;392(6678):825-8
PMID:39746995 - DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts.
Kuś K et al. Nat Commun 2025 Jan 02;16(1):10
PMID:29996109 - Quantitative Phosphoproteomics Reveals the Signaling Dynamics of Cell-Cycle Kinases in the Fission Yeast Schizosaccharomyces pombe.
Swaffer MP et al. Cell Rep 2018 Jul 10;24(2):503-514
PMID:8190062 - Molecular analysis of the dhp1+ gene of Schizosaccharomyces pombe: an essential gene that has homology to the DST2 and RAT1 genes of Saccharomyces cerevisiae.
Sugano S et al. Mol Gen Genet 1994 Apr;243(1):1-8
PMID:32841241 - Hypomodified tRNA in evolutionarily distant yeasts can trigger rapid tRNA decay to activate the general amino acid control response, but with different consequences.
De Zoysa T et al. PLoS Genet 2020 Aug;16(8):e1008893
GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:16823372 - ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe.
Matsuyama A et al. Nat Biotechnol 2006 Jul;24(7):841-7
PMID:24493644 - lncRNA recruits RNAi and the exosome to dynamically regulate pho1 expression in response to phosphate levels in fission yeast.
Shah S et al. Genes Dev 2014 Feb 01;28(3):231-44
PMID:31883795 - Positioning Heterochromatin at the Nuclear Periphery Suppresses Histone Turnover to Promote Epigenetic Inheritance.
Holla S et al. Cell 2020 Jan 09;180(1):150-164.e15
PMID:26631744 - Conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing.
Chalamcharla VR et al. Proc Natl Acad Sci U S A 2015 Dec 22;112(51):15548-55
PMID:28367989 - The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA.
Wittmann S et al. Nat Commun 2017 Apr 03;8:14861
PMID:19194460 - Structure and function of the 5'-->3' exoribonuclease Rat1 and its activating partner Rai1.
Xiang S et al. Nature 2009 Apr 09;458(7239):784-8
PMID:7885830 - Characterization of cDNA encoding mouse homolog of fission yeast dhp1+ gene: structural and functional conservation.
Shobuike T et al. Nucleic Acids Res 1995 Feb 11;23(3):357-61
PMID:23101633 - Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells.
Marguerat S et al. Cell 2012 Oct 26;151(3):671-83