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protein coding gene - mtr4 (SPAC6F12.16c) - TRAMP complex ATP-dependent RNA helicase subunit Mtr4

Gene summary

Standard name
mtr4
Systematic ID
SPAC6F12.16c
Product
TRAMP complex ATP-dependent RNA helicase subunit Mtr4
Organism
Schizosaccharomyces pombe (fission yeast)
UniProt ID
O14232
ORFeome ID
30/30D09
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome I: 1344924..1348489 reverse strand

Annotation

GO biological process

GO:0000460 - maturation of 5.8S rRNA

References:

GO:0043634 - polyadenylation-dependent ncRNA catabolic process

References:

GO:0006401 - RNA catabolic process

References:

GO:0140746 - siRNA catabolic process

References:

GO:0071038 - TRAMP-dependent tRNA surveillance pathway

References:

GO cellular component

GO:0005730 - nucleolus

References:

GO:0005634 - nucleus

References:

GO:0031499 - TRAMP complex

References:

GO molecular function

GO:0005524 - ATP binding

References:

GO:0016887 - ATP hydrolysis activity

References:

GO:0003723 - RNA binding

References:

GO:0004532 - RNA exonuclease activity

References:

GO:0003724 - RNA helicase activity

References:

Modification

MOD:00046 - O-phospho-L-serine

References:

Multi-locus phenotype

FYPO:0001908 - increased pre-mRNA level

References:

Genotypes:

Protein features

PBO:0111747 - DEAD/DEAH box helicase

Qualitative gene expression

PomGeneEx:0000019 - protein level decreased

References:

PomGeneEx:0000012 - RNA level decreased

References:

Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

References:

Single locus phenotype

FYPO:0007336 - abolished chromatin silencing at silent mating-type cassette

References:

Genotypes:

FYPO:0004573 - increased telomeric transcript level

References:

Genotypes:

FYPO:0002420 - inviable after spore germination, single cell division, abnormal cell shape

References:

Genotypes:

FYPO:0002151 - inviable spore

References:

Genotypes:

FYPO:0002061 - inviable vegetative cell population

References:

Genotypes:

FYPO:0003620 - normal pre-mRNA level

References:

Genotypes:

FYPO:0006279 - normal termination of RNA polymerase II transcription

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
PF00271Helicase_CHelicase_C-likePFAM
PF13234MTR4_beta-barrelBeta-barrel_MTR4PFAM
PF21408MTR4-like_stalkMTR4-like_stalkPFAM
PF08148DSHCTSki2/MTR4_CPFAM
PF00270DEADDEAD/DEAH_box_helicase_domPFAM
cd18024DEXHc_Mtr4-likeCDD
cd18795SF2_C_Ski2CDD
cd13154KOW_Mtr4CDD
PS51194HELICASE_CTERHelicase_C-likePROSITE_PROFILES
PS51192HELICASE_ATP_BIND_1Helicase_ATP-bdPROSITE_PROFILES
SM00487ultradead3Helicase_ATP-bdSMART
SM01142DSHCT_2Ski2/MTR4_CSMART
SM00490helicmild6Helicase_C-likeSMART
G3DSA:3.40.50.300:FF:000083FUNFAM
G3DSA:2.40.30.300:FF:000001FUNFAM
G3DSA:3.40.50.300:FF:000141FUNFAM
G3DSA:1.10.3380.30:FF:000002FUNFAM
SSF52540P-loop containing nucleoside triphosphate hydrolasesP-loop_NTPaseSUPERFAMILY
G3DSA:3.40.50.300P-loop_NTPaseGENE3D
G3DSA:1.10.3380.30GENE3D
G3DSA:2.40.30.300GENE3D
PTHR12131ATP-DEPENDENT RNA AND DNA HELICASESUPV3-likePANTHER
PIRSF005198SKI2FRH-likePIRSF
CoilCoilCOILS
mobidb-lite-Disorderdisorder_predictionMOBIDB-Disorder
mobidb-lite-Polyampholytedisorder_predictionMOBIDB-Polyampholyte

Orthologs

References / Literature

PMID:29906447 - Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex.
Weick EM et al. Cell 2018 Jun 14;173(7):1663-1677.e21
PMID:31064814 - Proximity-dependent biotinylation mediated by TurboID to identify protein-protein interaction networks in yeast.
Larochelle M et al. J Cell Sci 2019 May 31;132(11)
GO_REF:0000002 - Comments
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
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
PMID:19336419 - Cotranscriptional recruitment of the nuclear poly(A)-binding protein Pab2 to nascent transcripts and association with translating mRNPs.
Lemieux C et al. Nucleic Acids Res 2009 Jun;37(10):3418-30
PMID:26167880 - SR protein kinases promote splicing of nonconsensus introns.
Lipp JJ et al. Nat Struct Mol Biol 2015 Aug;22(8):611-7
PMID:22681890 - Hierarchical modularity and the evolution of genetic interactomes across species.
Ryan CJ et al. Mol Cell 2012 Jun 08;46(5):691-704
PMID:21712547 - Mitotic substrates of the kinase aurora with roles in chromatin regulation identified through quantitative phosphoproteomics of fission yeast.
Koch A et al. Sci Signal 2011 Jun 28;4(179):rs6
PMID:38051102 - Fission Yeast TORC1 Promotes Cell Proliferation through Sfp1, a Transcription Factor Involved in Ribosome Biogenesis.
Tai YT et al. Mol Cell Biol 2023 Dec 05;:1-18
GO_REF:0000024 - Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity.
PMID:17512405 - RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing.
Bühler M et al. Cell 2007 May 18;129(4):707-21
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:21436456 - Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA.
Zhang K et al. Science 2011 Mar 25;331(6024):1624-7
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:25240800 - The RNA exosome promotes transcription termination of backtracked RNA polymerase II.
Lemay JF et al. Nat Struct Mol Biol 2014 Oct;21(10):919-26
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:24210919 - Mtr4-like protein coordinates nuclear RNA processing for heterochromatin assembly and for telomere maintenance.
Lee NN et al. Cell 2013 Nov 21;155(5):1061-74
PMID:24081329 - Poly(A) tail-mediated gene regulation by opposing roles of Nab2 and Pab2 nuclear poly(A)-binding proteins in pre-mRNA decay.
Grenier St-Sauveur V et al. Mol Cell Biol 2013 Dec;33(23):4718-31
PMID:16537923 - Sterol regulatory element binding protein is a principal regulator of anaerobic gene expression in fission yeast.
Todd BL et al. Mol Cell Biol 2006 Apr;26(7):2817-31
PMID:33313903 - Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast.
Rubio A et al. Nucleic Acids Res 2021 Jan 11;49(1):383-399
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:20403971 - Proteomic and functional analysis of the noncanonical poly(A) polymerase Cid14.
Keller C et al. RNA 2010 Jun;16(6):1124-9
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: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
GO_REF:0000033 - Annotation inferences using phylogenetic trees
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: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:30321377 - Proteomic profiling and functional characterization of post-translational modifications of the fission yeast RNA exosome.
Telekawa C et al. Nucleic Acids Res 2018 Nov 30;46(21):11169-11183
PMID:26896847 - Ensembl comparative genomics resources.
Herrero J et al. Database (Oxford) 2016;2016
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:21981922 - A Pre-mRNA degradation pathway that selectively targets intron-containing genes requires the nuclear poly(A)-binding protein.
Lemieux C et al. Mol Cell 2011 Oct 07;44(1):108-19
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:22965128 - The THO complex cooperates with the nuclear RNA surveillance machinery to control small nucleolar RNA expression.
Larochelle M et al. Nucleic Acids Res 2012 Nov 01;40(20):10240-53