LSM4_ARATH
ID LSM4_ARATH Reviewed; 129 AA.
AC F4K4E3; Q8LAC6; Q8RWJ9;
DT 07-JAN-2015, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 69.
DE RecName: Full=Sm-like protein LSM4 {ECO:0000305};
DE Short=AtLSM4 {ECO:0000303|PubMed:23620288};
DE AltName: Full=Protein EMBRYO DEFECTIVE 1644 {ECO:0000305};
DE AltName: Full=U6 snRNA-associated Sm-like protein LSM4 {ECO:0000305};
GN Name=LSM4 {ECO:0000303|PubMed:23221597}; Synonyms=EMB1644 {ECO:0000305};
GN OrderedLocusNames=At5g27720 {ECO:0000312|Araport:AT5G27720};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP METHYLATION BY PMRT15/SKB1, AND DISRUPTION PHENOTYPE.
RX PubMed=21258002; DOI=10.1105/tpc.110.081356;
RA Zhang Z., Zhang S., Zhang Y., Wang X., Li D., Li Q., Yue M., Li Q.,
RA Zhang Y.E., Xu Y., Xue Y., Chong K., Bao S.;
RT "Arabidopsis floral initiator SKB1 confers high salt tolerance by
RT regulating transcription and pre-mRNA splicing through altering histone
RT H4R3 and small nuclear ribonucleoprotein LSM4 methylation.";
RL Plant Cell 23:396-411(2011).
RN [6]
RP FUNCTION, SUBUNIT, INTERACTION WITH LSM1A; LSM7 AND LSM8, SUBCELLULAR
RP LOCATION, TISSUE SPECIFICITY, AND GENE FAMILY.
RX PubMed=23221597; DOI=10.1105/tpc.112.103697;
RA Perea-Resa C., Hernandez-Verdeja T., Lopez-Cobollo R.,
RA del Mar Castellano M., Salinas J.;
RT "LSM proteins provide accurate splicing and decay of selected transcripts
RT to ensure normal Arabidopsis development.";
RL Plant Cell 24:4930-4947(2012).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, SUBUNIT, AND TISSUE
RP SPECIFICITY.
RX PubMed=23620288; DOI=10.1093/nar/gkt296;
RA Golisz A., Sikorski P.J., Kruszka K., Kufel J.;
RT "Arabidopsis thaliana LSM proteins function in mRNA splicing and
RT degradation.";
RL Nucleic Acids Res. 41:6232-6249(2013).
CC -!- FUNCTION: Component of LSM protein complexes, which are involved in RNA
CC processing. Component of the cytoplasmic LSM1-LSM7 complex which is
CC involved in mRNA degradation by promoting decapping and leading to
CC accurate 5'-3' mRNA decay. The cytoplasmic LSM1-LSM7 complex regulates
CC developmental gene expression by the decapping of specific development-
CC related transcripts. Component of the nuclear LSM2-LSM8 complex which
CC is involved splicing nuclear mRNAs. LSM2-LSM8 binds directly to the U6
CC small nuclear RNAs (snRNAs) and is essential for accurate splicing of
CC selected development-related mRNAs through the stabilization of the
CC spliceosomal U6 snRNA. Plays a critical role in the regulation of
CC development-related gene expression. {ECO:0000269|PubMed:23221597,
CC ECO:0000269|PubMed:23620288}.
CC -!- SUBUNIT: Component of the heptameric LSM1-LSM7 complex that forms a
CC seven-membered ring structure with a donut shape. The LSM subunits are
CC arranged in the order LSM1, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4
CC (PubMed:23221597, PubMed:23620288). LSM4 subunit interacts only with
CC its two neighboring subunits, LSM1A or LSM1B and LSM7
CC (PubMed:23221597). Component of the heptameric LSM2-LSM8 complex that
CC forms a seven-membered ring structure with a donut shape. The LSM
CC subunits are arranged in the order LSM8, LSM2, LSM3, LSM6, LSM5, LSM7
CC and LSM4 (PubMed:23221597, PubMed:23620288). LSM4 subunit interacts
CC only with its two neighboring subunits, LSM8 and LSM7
CC (PubMed:23221597). {ECO:0000269|PubMed:23221597,
CC ECO:0000269|PubMed:23620288}.
CC -!- INTERACTION:
CC F4K4E3; O23160: MYB73; NbExp=3; IntAct=EBI-16419411, EBI-25506855;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:23221597}. Nucleus
CC {ECO:0000269|PubMed:23221597}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves, stems, flowers and
CC siliques. {ECO:0000269|PubMed:23221597, ECO:0000269|PubMed:23620288}.
CC -!- PTM: Methylated by PMRT15/SKB1 in response to salt stress or abscisic
CC acid (ABA) treatment. {ECO:0000269|PubMed:21258002}.
CC -!- DISRUPTION PHENOTYPE: Severe developmental retardation leading to plant
CC death. {ECO:0000269|PubMed:21258002}.
CC -!- SIMILARITY: Belongs to the snRNP Sm proteins family. {ECO:0000305}.
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DR EMBL; AC069556; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002688; AED93718.1; -; Genomic_DNA.
DR EMBL; AY093040; AAM13039.1; -; mRNA.
DR EMBL; AY128942; AAM91342.1; -; mRNA.
DR EMBL; AY087911; AAM65462.1; -; mRNA.
DR RefSeq; NP_198124.1; NM_122654.4.
DR AlphaFoldDB; F4K4E3; -.
DR SMR; F4K4E3; -.
DR ComplexPortal; CPX-1308; LSM1-7-PAT1 complex, variant LSM1A-LSM3A-LSM6A-PAT1.
DR ComplexPortal; CPX-1309; LSM2-8 complex, variant LSM3A-LSM6A.
DR ComplexPortal; CPX-1345; LSM1-7-PAT1 complex, variant LSM1A-LSM3B-LSM6B-PAT1.
DR ComplexPortal; CPX-1346; LSM1-7-PAT1 complex, variant LSM1A-LSM3B-LSM6A-PAT1.
DR ComplexPortal; CPX-1347; LSM1-7-PAT1 complex, variant LSM1B-LSM3A-LSM6A-PAT1.
DR ComplexPortal; CPX-1348; LSM1-7-PAT1 complex, variant LSM1B-LSM3B-LSM6A-PAT1.
DR ComplexPortal; CPX-1349; LSM1-7-PAT1 complex, variant LSM1B-LSM3B-LSM6B-PAT1.
DR ComplexPortal; CPX-1350; LSM1-7-PAT1 complex, variant LSM1B-LSM3A-LSM6B-PAT1.
DR ComplexPortal; CPX-1351; LSM1-7-PAT1 complex, variant LSM1A-LSM3A-LSM6B-PAT1.
DR ComplexPortal; CPX-1352; LSM2-8 complex, variant LSM3A-LSM6B.
DR ComplexPortal; CPX-1353; LSM2-8 complex, variant LSM3B-LSM6A.
DR ComplexPortal; CPX-1354; LSM2-8 complex, variant LSM3B-LSM6B.
DR ComplexPortal; CPX-1391; LSM1-7-PAT1 complex, variant LSM1A-LSM3A-LSM6A-PAT1H1.
DR ComplexPortal; CPX-1392; LSM1-7-PAT1 complex, variant LSM1A-LSM3A-LSM6B-PAT1H1.
DR ComplexPortal; CPX-1393; LSM1-7-PAT1 complex, variant LSM1A-LSM3B-LSM6A-PAT1H1.
DR ComplexPortal; CPX-1394; LSM1-7-PAT1 complex, variant LSM1A-LSM3B-LSM6B-PAT1H1.
DR ComplexPortal; CPX-1395; LSM1-7-PAT1 complex, variant LSM1B-LSM3A-LSM6A-PAT1H1.
DR ComplexPortal; CPX-1396; LSM1-7-PAT1 complex, variant LSM1B-LSM3A-LSM6B-PAT1H1.
DR ComplexPortal; CPX-1397; LSM1-7-PAT1 complex, variant LSM1B-LSM3B-LSM6A-PAT1H1.
DR ComplexPortal; CPX-1398; LSM1-7-PAT1 complex, variant LSM1B-LSM3B-LSM6B-PAT1H1.
DR ComplexPortal; CPX-1399; LSM1-7-PAT1 complex, variant LSM1A-LSM3A-LSM6A-PAT1H2.
DR ComplexPortal; CPX-1400; LSM1-7-PAT1 complex, variant LSM1A-LSM3A-LSM6B-PAT1H2.
DR ComplexPortal; CPX-1401; LSM1-7-PAT1 complex, variant LSM1A-LSM3B-LSM6A-PAT1H2.
DR ComplexPortal; CPX-1402; LSM1-7-PAT1 complex, variant LSM1A-LSM3B-LSM6B-PAT1H2.
DR ComplexPortal; CPX-1403; LSM1-7-PAT1 complex, variant LSM1B-LSM3A-LSM6A-PAT1H2.
DR ComplexPortal; CPX-1404; LSM1-7-PAT1 complex, variant LSM1B-LSM3A-LSM6B-PAT1H2.
DR ComplexPortal; CPX-1405; LSM1-7-PAT1 complex, variant LSM1B-LSM3B-LSM6A-PAT1H2.
DR ComplexPortal; CPX-1406; LSM1-7-PAT1 complex, variant LSM1B-LSM3B-LSM6B-PAT1H2.
DR IntAct; F4K4E3; 1.
DR STRING; 3702.AT5G27720.1; -.
DR iPTMnet; F4K4E3; -.
DR PaxDb; F4K4E3; -.
DR PRIDE; F4K4E3; -.
DR ProteomicsDB; 238574; -.
DR EnsemblPlants; AT5G27720.1; AT5G27720.1; AT5G27720.
DR GeneID; 832834; -.
DR Gramene; AT5G27720.1; AT5G27720.1; AT5G27720.
DR KEGG; ath:AT5G27720; -.
DR Araport; AT5G27720; -.
DR TAIR; locus:2180295; AT5G27720.
DR eggNOG; KOG3293; Eukaryota.
DR HOGENOM; CLU_099537_2_1_1; -.
DR InParanoid; F4K4E3; -.
DR OMA; GTSMGKM; -.
DR OrthoDB; 1561576at2759; -.
DR PRO; PR:F4K4E3; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; F4K4E3; baseline and differential.
DR Genevisible; F4K4E3; AT.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:1990726; C:Lsm1-7-Pat1 complex; IC:ComplexPortal.
DR GO; GO:0120115; C:Lsm2-8 complex; IMP:ComplexPortal.
DR GO; GO:0005634; C:nucleus; IDA:ComplexPortal.
DR GO; GO:0000932; C:P-body; IBA:GO_Central.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0005681; C:spliceosomal complex; IEA:UniProtKB-KW.
DR GO; GO:0097526; C:spliceosomal tri-snRNP complex; IBA:GO_Central.
DR GO; GO:0005688; C:U6 snRNP; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0017070; F:U6 snRNA binding; IBA:GO_Central.
DR GO; GO:0000290; P:deadenylation-dependent decapping of nuclear-transcribed mRNA; IC:ComplexPortal.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IMP:ComplexPortal.
DR GO; GO:0033962; P:P-body assembly; IBA:GO_Central.
DR GO; GO:0000387; P:spliceosomal snRNP assembly; IBA:GO_Central.
DR CDD; cd01723; LSm4; 1.
DR InterPro; IPR034101; Lsm4.
DR InterPro; IPR027141; LSm4/Sm_D1/D3.
DR InterPro; IPR001163; LSM_dom_euk/arc.
DR InterPro; IPR010920; LSM_dom_sf.
DR PANTHER; PTHR23338; PTHR23338; 1.
DR Pfam; PF01423; LSM; 1.
DR SMART; SM00651; Sm; 1.
DR SUPFAM; SSF50182; SSF50182; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; mRNA processing; mRNA splicing; Nucleus; Reference proteome;
KW Ribonucleoprotein; RNA-binding; Spliceosome.
FT CHAIN 1..129
FT /note="Sm-like protein LSM4"
FT /id="PRO_0000431646"
FT REGION 79..129
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 79..106
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 7
FT /note="L -> F (in Ref. 3; AAM13039/AAM91342)"
FT /evidence="ECO:0000305"
FT CONFLICT 101
FT /note="V -> L (in Ref. 4; AAM65462)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 129 AA; 14323 MW; 2B6658972F9B1DE9 CRC64;
MLPLSLLKTA QGHPMLVELK NGETYNGHLV NCDTWMNIHL REVICTSKDG DRFWRMPECY
IRGNTIKYLR VPDEVIDKVQ EEKTRTDRKP PGVGRGRGRG VDDGGARGRG RGTSMGKMGG
NRGAGRGRG
