HMGB1_ARATH
ID HMGB1_ARATH Reviewed; 178 AA.
AC O49595; Q3EAL6;
DT 02-NOV-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1998, sequence version 1.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=High mobility group B protein 1;
DE AltName: Full=High mobility group protein A;
DE Short=AtHMGalpha;
DE Short=HMG alpha;
DE AltName: Full=Nucleosome/chromatin assembly factor group D 01;
DE Short=Nucleosome/chromatin assembly factor group D 1;
GN Name=HMGB1; Synonyms=HMGA, HMGALPHA, NFD01, NFD1, ORF13;
GN OrderedLocusNames=At3g51880; ORFNames=ATEM1.13;
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 [MRNA] (ISOFORM 1), FUNCTION, AND TISSUE SPECIFICITY.
RC TISSUE=Leaf;
RX PubMed=9461286; DOI=10.1111/j.1432-1033.1997.00646.x;
RA Stemmer C., Ritt C., Igloi G.L., Grimm R., Grasser K.D.;
RT "Variability in Arabidopsis thaliana chromosomal high-mobility-group-1-like
RT proteins.";
RL Eur. J. Biochem. 250:646-652(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10645728; DOI=10.1023/a:1006395324818;
RA Comella P., Wu H.-J., Laudie M., Berger C., Cooke R., Delseny M.,
RA Grellet F.;
RT "Fine sequence analysis of 60 kb around the Arabidopsis thaliana AtEm1
RT locus on chromosome III.";
RL Plant Mol. Biol. 41:687-700(1999).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia; TISSUE=Rosette leaf;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [6]
RP PHOSPHORYLATION.
RX PubMed=12653554; DOI=10.1021/bi027350d;
RA Stemmer C., Leeming D.J., Franssen L., Grimm R., Grasser K.D.;
RT "Phosphorylation of maize and Arabidopsis HMGB proteins by protein kinase
RT CK2alpha.";
RL Biochemistry 42:3503-3508(2003).
RN [7]
RP SUBCELLULAR LOCATION, AND FUNCTION.
RX PubMed=17114349; DOI=10.1105/tpc.106.047274;
RA Launholt D., Merkle T., Houben A., Schulz A., Grasser K.D.;
RT "Arabidopsis chromatin-associated HMGA and HMGB use different nuclear
RT targeting signals and display highly dynamic localization within the
RT nucleus.";
RL Plant Cell 18:2904-2918(2006).
RN [8]
RP TISSUE SPECIFICITY.
RX PubMed=17316617; DOI=10.1016/j.febslet.2007.02.015;
RA Launholt D., Groenlund J.T., Nielsen H.K., Grasser K.D.;
RT "Overlapping expression patterns among the genes encoding Arabidopsis
RT chromosomal high mobility group (HMG) proteins.";
RL FEBS Lett. 581:1114-1118(2007).
RN [9]
RP TISSUE SPECIFICITY, AND INDUCTION BY SALT.
RX PubMed=17169924; DOI=10.1093/pcp/pcl057;
RA Kwak K.J., Kim J.Y., Kim Y.O., Kang H.;
RT "Characterization of transgenic Arabidopsis plants overexpressing high
RT mobility group B proteins under high salinity, drought or cold stress.";
RL Plant Cell Physiol. 48:221-231(2007).
RN [10]
RP SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=18822296; DOI=10.1016/j.jmb.2008.09.014;
RA Lildballe D.L., Pedersen D.S., Kalamajka R., Emmersen J., Houben A.,
RA Grasser K.D.;
RT "The expression level of the chromatin-associated HMGB1 protein influences
RT growth, stress tolerance, and transcriptome in Arabidopsis.";
RL J. Mol. Biol. 384:9-21(2008).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-146, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Root;
RX PubMed=18433157; DOI=10.1021/pr8000173;
RA de la Fuente van Bentem S., Anrather D., Dohnal I., Roitinger E.,
RA Csaszar E., Joore J., Buijnink J., Carreri A., Forzani C., Lorkovic Z.J.,
RA Barta A., Lecourieux D., Verhounig A., Jonak C., Hirt H.;
RT "Site-specific phosphorylation profiling of Arabidopsis proteins by mass
RT spectrometry and peptide chip analysis.";
RL J. Proteome Res. 7:2458-2470(2008).
RN [12]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-146, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA Rathjen J.P., Peck S.C.;
RT "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT thaliana.";
RL J. Proteomics 72:439-451(2009).
RN [13]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-137 AND SER-146, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [14]
RP REVIEW.
RX PubMed=20123078; DOI=10.1016/j.bbagrm.2009.11.004;
RA Pedersen D.S., Grasser K.D.;
RT "The role of chromosomal HMGB proteins in plants.";
RL Biochim. Biophys. Acta 1799:171-174(2010).
CC -!- FUNCTION: Binds preferentially double-stranded DNA. Modulates general
CC plant growth and stress tolerance. Confers sensitivity to salt and
CC genotoxic (methyl methanesulfonate, MMS) stresses.
CC {ECO:0000269|PubMed:17114349, ECO:0000269|PubMed:9461286}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00267,
CC ECO:0000269|PubMed:17114349, ECO:0000269|PubMed:18822296}.
CC Note=Displays a highly dynamic speckle distribution pattern in
CC interphase chromatin but does not associate with mitotic chromosomes.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=O49595-1; Sequence=Displayed;
CC Name=2;
CC IsoId=O49595-2; Sequence=VSP_039939;
CC -!- TISSUE SPECIFICITY: Expressed in cotyledons, roots, stems, leaves and
CC flowers (excluding pedicels). {ECO:0000269|PubMed:17169924,
CC ECO:0000269|PubMed:17316617, ECO:0000269|PubMed:9461286}.
CC -!- INDUCTION: Down-regulated by salt stress.
CC {ECO:0000269|PubMed:17169924}.
CC -!- DISRUPTION PHENOTYPE: Slightly delayed and reduced germination rate.
CC Reduced root length. Enhanced sensitivity to methyl methanesulfonate
CC (MMS). {ECO:0000269|PubMed:18822296}.
CC -!- SIMILARITY: Belongs to the HMGB family. {ECO:0000305}.
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DR EMBL; Y14071; CAA74400.1; -; mRNA.
DR EMBL; AF049236; AAC14415.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE78855.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE78856.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE78857.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM65542.1; -; Genomic_DNA.
DR EMBL; AY056373; AAL08229.1; -; mRNA.
DR EMBL; AY113172; AAM47475.1; -; mRNA.
DR EMBL; AK316819; BAH19531.1; -; mRNA.
DR PIR; T51159; T51159.
DR RefSeq; NP_001078269.1; NM_001084800.2. [O49595-1]
DR RefSeq; NP_001327501.1; NM_001339538.1. [O49595-1]
DR RefSeq; NP_190756.1; NM_115047.3. [O49595-1]
DR RefSeq; NP_974413.1; NM_202684.3. [O49595-2]
DR AlphaFoldDB; O49595; -.
DR SMR; O49595; -.
DR BioGRID; 9669; 4.
DR IntAct; O49595; 4.
DR STRING; 3702.AT3G51880.2; -.
DR iPTMnet; O49595; -.
DR PaxDb; O49595; -.
DR PRIDE; O49595; -.
DR ProteomicsDB; 230339; -. [O49595-1]
DR EnsemblPlants; AT3G51880.1; AT3G51880.1; AT3G51880. [O49595-1]
DR EnsemblPlants; AT3G51880.2; AT3G51880.2; AT3G51880. [O49595-2]
DR EnsemblPlants; AT3G51880.3; AT3G51880.3; AT3G51880. [O49595-1]
DR EnsemblPlants; AT3G51880.5; AT3G51880.5; AT3G51880. [O49595-1]
DR GeneID; 824351; -.
DR Gramene; AT3G51880.1; AT3G51880.1; AT3G51880. [O49595-1]
DR Gramene; AT3G51880.2; AT3G51880.2; AT3G51880. [O49595-2]
DR Gramene; AT3G51880.3; AT3G51880.3; AT3G51880. [O49595-1]
DR Gramene; AT3G51880.5; AT3G51880.5; AT3G51880. [O49595-1]
DR KEGG; ath:AT3G51880; -.
DR Araport; AT3G51880; -.
DR TAIR; locus:2074368; AT3G51880.
DR eggNOG; KOG0381; Eukaryota.
DR InParanoid; O49595; -.
DR OMA; KTHYERQ; -.
DR OrthoDB; 1641977at2759; -.
DR PhylomeDB; O49595; -.
DR PRO; PR:O49595; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; O49595; baseline and differential.
DR Genevisible; O49595; AT.
DR GO; GO:0000785; C:chromatin; TAS:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003682; F:chromatin binding; TAS:TAIR.
DR GO; GO:0003677; F:DNA binding; IDA:TAIR.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; ISS:TAIR.
DR GO; GO:0030527; F:structural constituent of chromatin; TAS:TAIR.
DR GO; GO:0006325; P:chromatin organization; TAS:TAIR.
DR Gene3D; 1.10.30.10; -; 1.
DR InterPro; IPR009071; HMG_box_dom.
DR InterPro; IPR036910; HMG_box_dom_sf.
DR InterPro; IPR031061; HMGB_plant.
DR PANTHER; PTHR46261; PTHR46261; 1.
DR Pfam; PF00505; HMG_box; 1.
DR SMART; SM00398; HMG; 1.
DR SUPFAM; SSF47095; SSF47095; 1.
DR PROSITE; PS50118; HMG_BOX_2; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; DNA-binding; Nucleus; Phosphoprotein;
KW Reference proteome.
FT CHAIN 1..178
FT /note="High mobility group B protein 1"
FT /id="PRO_0000399927"
FT DNA_BIND 53..122
FT /note="HMG box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00267"
FT REGION 1..59
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 75..178
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..54
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 98..141
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 142..178
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 137
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT MOD_RES 146
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18433157,
FT ECO:0007744|PubMed:19245862, ECO:0007744|PubMed:19376835"
FT VAR_SEQ 148
FT /note="E -> EVTIPLSN (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:19423640"
FT /id="VSP_039939"
SQ SEQUENCE 178 AA; 20265 MW; 2C1130786210828B CRC64;
MKTAKGKDKV KTTKEALKPV DDRKVGKRKA PAEKPTKRET RKEKKAKKDP NKPKRAPSAF
FVFLEDFRVT FKKENPNVKA VSAVGKAGGQ KWKSMSQAEK APYEEKAAKR KAEYEKQMDA
YNKNLEEGSD ESEKSRSEIN DEDEASGEEE LLEKEAAGDD EEEEEEEDDD DDDDEEED
