RIK1_SCHPO
ID RIK1_SCHPO Reviewed; 1040 AA.
AC Q10426; Q9USN9; Q9UUL7;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 21-FEB-2001, sequence version 2.
DT 25-MAY-2022, entry version 158.
DE RecName: Full=Chromatin modification-related protein rik1;
DE AltName: Full=Silencing protein rik1;
GN Name=rik1; ORFNames=SPCC11E10.08;
OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina;
OC Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae;
OC Schizosaccharomyces.
OX NCBI_TaxID=284812;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=EG355;
RA Nielsen O.;
RT "The rik1 gene from S. pombe required for formation of silent
RT heterochromatin encodes a protein related to Xeroderma pigmentosum group E
RT DNA-binding protein.";
RL Submitted (MAR-1999) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=972 / ATCC 24843;
RX PubMed=11859360; DOI=10.1038/nature724;
RA Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A.,
RA Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S.,
RA Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.,
RA Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S.,
RA Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S.,
RA Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D.,
RA Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P.,
RA Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K.,
RA O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M.,
RA Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N.,
RA Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A.,
RA Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R.,
RA Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M.,
RA Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A.,
RA Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A.,
RA Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H.,
RA Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S.,
RA Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C.,
RA Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A.,
RA Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M.,
RA del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S.,
RA Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R.,
RA Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G.,
RA Nurse P.;
RT "The genome sequence of Schizosaccharomyces pombe.";
RL Nature 415:871-880(2002).
RN [3]
RP PARTIAL PROTEIN SEQUENCE, IDENTIFICATION IN THE RIK1-ASSOCIATED E3
RP UBIQUITIN LIGASE COMPLEX, AND FUNCTION.
RX PubMed=16024659; DOI=10.1101/gad.1328005;
RA Horn P.J., Bastie J.-N., Peterson C.L.;
RT "A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for
RT heterochromatin formation.";
RL Genes Dev. 19:1705-1714(2005).
RN [4]
RP FUNCTION.
RX PubMed=8138176; DOI=10.1093/genetics/136.1.53;
RA Ekwall K., Ruusala T.;
RT "Mutations in rik1, clr2, clr3 and clr4 genes asymmetrically derepress the
RT silent mating-type loci in fission yeast.";
RL Genetics 136:53-64(1994).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=7851795; DOI=10.1101/gad.9.2.218;
RA Allshire R.C., Nimmo E.R., Ekwall K., Javerzat J.-P., Cranston G.;
RT "Mutations derepressing silent centromeric domains in fission yeast disrupt
RT chromosome segregation.";
RL Genes Dev. 9:218-233(1995).
RN [6]
RP FUNCTION, AND INTERACTION WITH CHP1.
RX PubMed=10766735;
RA Partridge J.F., Borgstroem B., Allshire R.C.;
RT "Distinct protein interaction domains and protein spreading in a complex
RT centromere.";
RL Genes Dev. 14:783-791(2000).
RN [7]
RP FUNCTION.
RX PubMed=15372076; DOI=10.1038/sj.emboj.7600401;
RA Sadaie M., Iida T., Urano T., Nakayama J.;
RT "A chromodomain protein, Chp1, is required for the establishment of
RT heterochromatin in fission yeast.";
RL EMBO J. 23:3825-3835(2004).
RN [8]
RP FUNCTION.
RX PubMed=15197176; DOI=10.1083/jcb.200312061;
RA Tuzon C.T., Borgstroem B., Weilguny D., Egel R., Cooper J.P., Nielsen O.;
RT "The fission yeast heterochromatin protein Rik1 is required for telomere
RT clustering during meiosis.";
RL J. Cell Biol. 165:759-765(2004).
RN [9]
RP PROTEIN SEQUENCE OF 663-692 AND 922-965, AND INTERACTION WITH CUL4.
RX PubMed=16127433; DOI=10.1038/ncb1300;
RA Jia S., Kobayashi R., Grewal S.I.S.;
RT "Ubiquitin ligase component Cul4 associates with Clr4 histone
RT methyltransferase to assemble heterochromatin.";
RL Nat. Cell Biol. 7:1007-1013(2005).
RN [10]
RP SUBUNIT.
RX PubMed=17114925; DOI=10.4161/rna.2.3.2131;
RA Hong E.J., Villen J., Gerace E.L., Gygi S.P., Moazed D.;
RT "A cullin E3 ubiquitin ligase complex associates with Rik1 and the Clr4
RT histone H3-K9 methyltransferase and is required for RNAi-mediated
RT heterochromatin formation.";
RL RNA Biol. 2:106-111(2005).
RN [11]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=16823372; DOI=10.1038/nbt1222;
RA Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S.,
RA Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S.,
RA Yoshida M.;
RT "ORFeome cloning and global analysis of protein localization in the fission
RT yeast Schizosaccharomyces pombe.";
RL Nat. Biotechnol. 24:841-847(2006).
RN [12]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=18345014; DOI=10.1038/nsmb.1406;
RA Zhang K., Mosch K., Fischle W., Grewal S.I.;
RT "Roles of the Clr4 methyltransferase complex in nucleation, spreading and
RT maintenance of heterochromatin.";
RL Nat. Struct. Mol. Biol. 15:381-388(2008).
RN [13]
RP FUNCTION.
RX PubMed=31468675; DOI=10.15252/embr.201948111;
RA Oya E., Nakagawa R., Yoshimura Y., Tanaka M., Nishibuchi G., Machida S.,
RA Shirai A., Ekwall K., Kurumizaka H., Tagami H., Nakayama J.I.;
RT "H3K14 ubiquitylation promotes H3K9 methylation for heterochromatin
RT assembly.";
RL EMBO Rep. 20:E48111-E48111(2019).
CC -!- FUNCTION: Component of the Clr4 methyltransferase complex (ClrC) which
CC contributes to the establishment of heterochromatin by specifically
CC methylating histone H3 to form H3K9me (PubMed:16024659, PubMed:8138176,
CC PubMed:15372076). ClrC preferentially ubiquitylates H3K14 and ClrC-
CC mediated H3 ubiquitination promotes clr4 methyltransferase activity for
CC the methylation of H3K9 (PubMed:31468675). H3K9me represents a specific
CC tag for epigenetic transcriptional repression by recruiting swi6/HP1 to
CC methylated histones which leads to transcriptional silencing within
CC centromeric heterochromatin, telomeric regions and at the silent
CC mating-type loci (PubMed:16024659, PubMed:8138176, PubMed:7851795,
CC PubMed:10766735). Rik1 is involved in the RNAi-mediated targeting of
CC ClrC to heterochromatic repeat elements (PubMed:17114925,
CC PubMed:18345014). Rik1 has also a function in meiotic telomere
CC clustering (PubMed:15197176). {ECO:0000269|PubMed:10766735,
CC ECO:0000269|PubMed:15197176, ECO:0000269|PubMed:15372076,
CC ECO:0000269|PubMed:16024659, ECO:0000269|PubMed:17114925,
CC ECO:0000269|PubMed:18345014, ECO:0000269|PubMed:31468675,
CC ECO:0000269|PubMed:7851795, ECO:0000269|PubMed:8138176}.
CC -!- SUBUNIT: Component of the Clr4 methyltransferase complex (ClrC)
CC composed of at least clr4, rik1, pcu4, rbx1, raf1 and raf2. The cullin
CC pcu4, rik1, raf1, raf2 and the ring-box protein rbx1 are components of
CC an E3 ubiquitin ligase, whose activity is essential for heterochromatin
CC assembly. {ECO:0000269|PubMed:10766735, ECO:0000269|PubMed:16024659,
CC ECO:0000269|PubMed:16127433, ECO:0000269|PubMed:17114925}.
CC -!- INTERACTION:
CC Q10426; Q10103: chp1; NbExp=2; IntAct=EBI-1111936, EBI-421832;
CC Q10426; O60016: clr4; NbExp=3; IntAct=EBI-1111936, EBI-354657;
CC Q10426; P04913: htb1; NbExp=2; IntAct=EBI-1111936, EBI-1112091;
CC Q10426; O14122: pcu4; NbExp=3; IntAct=EBI-1111936, EBI-904890;
CC Q10426; O74910: raf1; NbExp=3; IntAct=EBI-1111936, EBI-904913;
CC Q10426; O94276: SPBP8B7.28c; NbExp=3; IntAct=EBI-1111936, EBI-2651917;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:16823372,
CC ECO:0000269|PubMed:18345014}. Cytoplasm, cytoskeleton, microtubule
CC organizing center, spindle pole body {ECO:0000269|PubMed:16823372}.
CC Chromosome {ECO:0000269|PubMed:18345014}.
CC -!- DISRUPTION PHENOTYPE: Cells show derepressed silent mating-type
CC cassettes. {ECO:0000269|PubMed:7851795}.
CC -!- SIMILARITY: Belongs to the DDB1 family. {ECO:0000305}.
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DR EMBL; AF136156; AAD24488.1; -; Genomic_DNA.
DR EMBL; CU329672; CAB57850.1; -; Genomic_DNA.
DR PIR; T40859; T40859.
DR RefSeq; NP_588204.1; NM_001023194.2.
DR AlphaFoldDB; Q10426; -.
DR SMR; Q10426; -.
DR BioGRID; 275623; 237.
DR DIP; DIP-35634N; -.
DR IntAct; Q10426; 9.
DR STRING; 4896.SPCC11E10.08.1; -.
DR MaxQB; Q10426; -.
DR PaxDb; Q10426; -.
DR EnsemblFungi; SPCC11E10.08.1; SPCC11E10.08.1:pep; SPCC11E10.08.
DR GeneID; 2539050; -.
DR KEGG; spo:SPCC11E10.08; -.
DR PomBase; SPCC11E10.08; rik1.
DR VEuPathDB; FungiDB:SPCC11E10.08; -.
DR eggNOG; KOG1897; Eukaryota.
DR HOGENOM; CLU_290548_0_0_1; -.
DR InParanoid; Q10426; -.
DR OMA; RDYLFVV; -.
DR PhylomeDB; Q10426; -.
DR PRO; PR:Q10426; -.
DR Proteomes; UP000002485; Chromosome III.
DR GO; GO:0005694; C:chromosome; IEA:UniProtKB-SubCell.
DR GO; GO:0043494; C:CLRC complex; IDA:PomBase.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-KW.
DR GO; GO:0005634; C:nucleus; HDA:PomBase.
DR GO; GO:0005816; C:spindle pole body; IEA:UniProtKB-SubCell.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR GO; GO:0006281; P:DNA repair; IEA:InterPro.
DR GO; GO:0031507; P:heterochromatin assembly; IMP:PomBase.
DR GO; GO:0045141; P:meiotic telomere clustering; IMP:PomBase.
DR Gene3D; 2.130.10.10; -; 3.
DR InterPro; IPR004871; Cleavage/polyA-sp_fac_asu_C.
DR InterPro; IPR018846; Cleavage/polyA-sp_fac_asu_N.
DR InterPro; IPR031297; DDB1.
DR InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR PANTHER; PTHR10644:SF3; PTHR10644:SF3; 1.
DR Pfam; PF03178; CPSF_A; 1.
DR Pfam; PF10433; MMS1_N; 1.
PE 1: Evidence at protein level;
KW Chromatin regulator; Chromosome; Cytoplasm; Cytoskeleton;
KW Direct protein sequencing; Nucleus; Reference proteome; Transcription;
KW Transcription regulation.
FT CHAIN 1..1040
FT /note="Chromatin modification-related protein rik1"
FT /id="PRO_0000097338"
FT CONFLICT 263
FT /note="G -> A (in Ref. 1; AAD24488)"
FT /evidence="ECO:0000305"
FT CONFLICT 446
FT /note="F -> N (in Ref. 1; AAD24488)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1040 AA; 118124 MW; 0C76BB59E1215BF1 CRC64;
MALCVHSFWA TAVDTATSCH FISSENCLVL LQALKINIYL CSEVHGLQFF TSIPLFSTVK
HIRPYRPPGL DRDYLFVVLN DDTYFSIYWD EDYQKVIVDH PPVRYRVTFP WNRNAKSYCL
VDLRMRAIFL SIDEISMICI RILSAEERLK TGRSIDSGFP FSFPVHLIYD MCILNDSSTP
TLVVLHSDGL DCYVTAFLLD LSSKSLGKGI RLFERVKPSM IMPFGKRGLL VFESLFIHCM
YRGNFVTING PCTTYMHWTP LKGQKMHYIV CDTNGYLFGV YSSILGKNKW SLVMERLPIP
PFDFITSLNS IHEGLLFIGS KNSESKLINL STLKDVDSIP NLGPIHDLLV LKNDIEKSFL
VCAGTPRNAS LIYFQHALKL DILGQTKISG ILRAMVLPSY PEHKLFLGFP SETVAFNIKE
DFQLELDPSL STKERTIALS GTNGEFVQVT STFLCIYDSA KRSRLVYIEK ITNAACYQEY
SAIVINGTAL AIFKKDTEVA RKVFESEISC LDFSAQFQIG VGFWSKQVMI LTFSDNSSIS
CAFQTNVPSL PRNIILEGVG VDRNLLLVSS GSGEFKSYVL FKNNLVFSET KHFGTTPVSF
RRFTMNIGTY IICNNDCPHM VYGFNGALCY MPLSMPQSYD VCQFRDNSGK DFLISVSLGG
LKFLQLNPLP ELTPRKVLLE HVPLQAIIFQ NKLLLRTLEN RYEDYESYKE NYHLELVDSY
DDNSFRVFSF TENERCEKVL KINESSLLVG TSIIEQDKLV PVNGRLILLE FEKELQSLKV
VSSMVLSAAV IDLGVYNDRY IVAFGQQVAI VKLTEERLMI DSRISLGSIV LQLIVEGNEI
AIADSIGRFT IMYFDGQKFI VVARYLFGEN IVKAALYEGT VYIIATNSGL LKLLRYNKDA
KNFNDRFICE SVYHLHDKVS KFQNFPITNT NSFLEPKMLF ATEIGAIGSI VSLKDKELEL
EELTRKIRKL KFSYLSSMDY ESIEADLISP VPFIDGDLVI DVKRWASSEL FRLCRSVEHR
ESLNSYQKVQ ALLEEIQSLC
