PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT2G30470.1
Common NameHSI2, T6B20.17, VAL1
Organism
Arabidopsis thaliana
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family B3
Protein Properties Length: 790aa    MW: 87001.7 Da    PI: 7.9045
Description high-level expression of sugar-inducible gene 2
Gene Model
Gene Model ID Type Source Coding Sequence
AT2G30470.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B357.82e-18295390194
                  EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EE CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvv 94 
                  f+k+l+ sd+++ grlvlpk +ae++   +++ e++ l+++d +gr+W+++++y  +++s++yvl+ G     ++  L++gD+v+F++++  +++l +
  AT2G30470.1 295 FEKTLSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLKIQDVRGREWTFQFRYwpNNNSRMYVLE-GVTPCIQSMMLQAGDTVTFSRVD-PGGKLIM 390
                  99**************************666678889*****************89999999***9.********************765.6665555 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.102.6E-28292402IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.49E-19292390IPR015300DNA-binding pseudobarrel domain
CDDcd100172.68E-23293390No hitNo description
SMARTSM010192.2E-22295395IPR003340B3 DNA binding domain
PROSITE profilePS5086310.659295396IPR003340B3 DNA binding domain
PfamPF023626.7E-16295390IPR003340B3 DNA binding domain
PROSITE profilePS5105012.856538588IPR011124Zinc finger, CW-type
PfamPF074962.0E-8544585IPR011124Zinc finger, CW-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009737Biological Processresponse to abscisic acid
GO:0009744Biological Processresponse to sucrose
GO:0010030Biological Processpositive regulation of seed germination
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:2000034Biological Processregulation of seed maturation
GO:0005634Cellular Componentnucleus
GO:0005739Cellular Componentmitochondrion
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0008270Molecular Functionzinc ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000084anatomyplant sperm cell
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025281anatomypollen
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 790 aa     Download sequence    Send to blast
MFEVKMGSKM CMNASCGTTS TVEWKKGWPL RSGLLADLCY RCGSAYESSL FCEQFHKDQS  60
GWRECYLCSK RLHCGCIASK VTIELMDYGG VGCSTCACCH QLNLNTRGEN PGVFSRLPMK  120
TLADRQHVNG ESGGRNEGDL FSQPLVMGGD KREEFMPHRG FGKLMSPEST TTGHRLDAAG  180
EMHESSPLQP SLNMGLAVNP FSPSFATEAV EGMKHISPSQ SNMVHCSASN ILQKPSRPAI  240
STPPVASKSA QARIGRPPVE GRGRGHLLPR YWPKYTDKEV QQISGNLNLN IVPLFEKTLS  300
ASDAGRIGRL VLPKACAEAY FPPISQSEGI PLKIQDVRGR EWTFQFRYWP NNNSRMYVLE  360
GVTPCIQSMM LQAGDTVTFS RVDPGGKLIM GSRKAANAGD MQGCGLTNGT STEDTSSSGV  420
TENPPSINGS SCISLIPKEL NGMPENLNSE TNGGRIGDDP TRVKEKKRTR TIGAKNKRLL  480
LHSEESMELR LTWEEAQDLL RPSPSVKPTI VVIEEQEIEE YDEPPVFGKR TIVTTKPSGE  540
QERWATCDDC SKWRRLPVDA LLSFKWTCID NVWDVSRCSC SAPEESLKEL ENVLKVGREH  600
KKRRTGESQA AKSQQEPCGL DALASAAVLG DTIGEPEVAT TTRHPRHRAG CSCIVCIQPP  660
SGKGRHKPTC GCTVCSTVKR RFKTLMMRRK KKQLERDVTA AEDKKKKDME LAESDKSKEE  720
KEVNTARIDL NSDPYNKEDV EAVAVEKEES RKRAIGQCSG VVAQDASDVL GVTELEGEGK  780
NVREEPRVSS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A7e-892734032132B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1678690KRRFKTLMMRRKK
2689706KKKQLERDVTAAEDKKKK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.274380.0flower| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1453616180.0
Genevisible267519_at0.0
Expression AtlasAT2G30470-
AtGenExpressAT2G30470-
ATTED-IIAT2G30470-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in flowers and at lower levels in roots, stems and leaves. {ECO:0000269|PubMed:15894743}.
Functional Description ? help Back to Top
Source Description
TAIRHSI2 is a member of a novel family of B3 domain proteins with a sequence similar to the ERF-associated amphiphilic repression (EAR) motif. It functions as an active repressor of the Spo minimal promoter (derived from a gene for sweet potato sporamin A1) through the EAR motif. It contains a plant-specific B3 DNA-binding domain. The Arabidopsis genome contains 42 genes with B3 domains which could be classified into three families that are represented by ABI3, ARF1 and RAV1. HSI2 belongs to the ABI3 family. It is expressed at similar levels in all organs. Treatment with 6% sucrose showed a slight increase in transcript levels after 24 h. No changes were observed after treatment with 50M ABA. It is localized in the nucleus via a nuclear localization sequence located in the fourth conserved region of the C-terminal B3 domain.
UniProtTranscriptional repressor of gene expression involved in embryonic pathways, such as LEC1, ABI3, and FUS3. Repressor of the sugar-inducible genes involved in the seed maturation program in seedlings. Plays an essential role in regulating the transition from seed maturation to seedling growth. Functionally redundant with VAL2/HSL1. {ECO:0000269|PubMed:15894743, ECO:0000269|PubMed:17158584, ECO:0000269|PubMed:17267611}.
Function -- GeneRIF ? help Back to Top
  1. These results indicate that HSI2 and related proteins are B3 domain-EAR motif active transcription repressors. [HSI2]
    [PMID: 15894743]
  2. A novel HSI2 mutant allele, hsi2-4, was identified that exhibits constitutively elevated luciferase expression while expression of the endogenous GSTF8 transcript remains unchanged. Microarray analysis indicated that the HSI2 PHD-like domain functions non-redundantly to repress a subset of seed maturation genes. [HSI2]
    [PMID: 22476218]
  3. These results implicate HSI2 as a negative regulator of drought stress response in Arabidopsis.
    [PMID: 24168327]
  4. HSI2 PHD-like domain in the regulation of gene expression involving histone modifications and DNA methylation-mediated epigenetic mechanisms.
    [PMID: 25367506]
  5. LEC1, LEC2 , and FUSCA3 transcripts are candidate targets of VAL1, acting through epigenetic and/or transcriptional repression.
    [PMID: 26678037]
  6. The results suggest that HSI2 recruits MED13 and HDA6 to suppress directly a subset of seed maturation genes post-germination.
    [PMID: 27335347]
  7. VAL1 localizes to the nucleation region in vivo, promoting histone deacetylation and FLOWERING LOCUS C transcriptional silencing, and interacts with components of the conserved apoptosis- and splicing-associated protein complex.
    [PMID: 27471304]
  8. VAL1 crystal structure provides insight into the important implication of VAL1-B3 domain in flowering process.
    [PMID: 29733847]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT2G30470.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDabscisic acid
Interaction ? help Back to Top
Source Intact With
IntActSearch Q8W4L5
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT2G30470
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB2065530.0AB206553.1 Arabidopsis thaliana HSI2 mRNA for transcription factor B3-EAR motif, complete cds.
GenBankAY0624920.0AY062492.1 Arabidopsis thaliana putative VP1/ABI3 family regulatory protein (At2g30470; T6B20.17) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_850146.10.0B3 domain-containing transcription repressor VAL1
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLA0A178VNU80.0A0A178VNU8_ARATH; VAL1
STRINGAT2G30470.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM69232440
Representative plantOGRP12361446
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. Berg A, et al.
    Ten members of the Arabidopsis gene family encoding methyl-CpG-binding domain proteins are transcriptionally active and at least one, AtMBD11, is crucial for normal development.
    Nucleic Acids Res., 2003. 31(18): p. 5291-304
    [PMID:12954765]
  3. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  4. Heazlewood JL, et al.
    Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components, provides assessment of targeting prediction programs, and indicates plant-specific mitochondrial proteins.
    Plant Cell, 2004. 16(1): p. 241-56
    [PMID:14671022]
  5. Tsukagoshi H,Saijo T,Shibata D,Morikami A,Nakamura K
    Analysis of a sugar response mutant of Arabidopsis identified a novel B3 domain protein that functions as an active transcriptional repressor.
    Plant Physiol., 2005. 138(2): p. 675-85
    [PMID:15894743]
  6. Li P, et al.
    Response diversity of Arabidopsis thaliana ecotypes in elevated [CO2] in the field.
    Plant Mol. Biol., 2006. 62(4-5): p. 593-609
    [PMID:16941220]
  7. Suzuki M,Wang HH,McCarty DR
    Repression of the LEAFY COTYLEDON 1/B3 regulatory network in plant embryo development by VP1/ABSCISIC ACID INSENSITIVE 3-LIKE B3 genes.
    Plant Physiol., 2007. 143(2): p. 902-11
    [PMID:17158584]
  8. Tsukagoshi H,Morikami A,Nakamura K
    Two B3 domain transcriptional repressors prevent sugar-inducible expression of seed maturation genes in Arabidopsis seedlings.
    Proc. Natl. Acad. Sci. U.S.A., 2007. 104(7): p. 2543-7
    [PMID:17267611]
  9. Swaminathan K,Peterson K,Jack T
    The plant B3 superfamily.
    Trends Plant Sci., 2008. 13(12): p. 647-55
    [PMID:18986826]
  10. Bowen AJ, et al.
    PAH-domain-specific interactions of the Arabidopsis transcription coregulator SIN3-LIKE1 (SNL1) with telomere-binding protein 1 and ALWAYS EARLY2 Myb-DNA binding factors.
    J. Mol. Biol., 2010. 395(5): p. 937-49
    [PMID:19962994]
  11. Van Leene J, et al.
    Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana.
    Mol. Syst. Biol., 2010. 6: p. 397
    [PMID:20706207]
  12. Hoppmann V, et al.
    The CW domain, a new histone recognition module in chromatin proteins.
    EMBO J., 2011. 30(10): p. 1939-52
    [PMID:21522130]
  13. Veerappan V, et al.
    A novel HSI2 mutation in Arabidopsis affects the PHD-like domain and leads to derepression of seed-specific gene expression.
    Planta, 2012. 236(1): p. 1-17
    [PMID:22476218]
  14. Wang F,Perry SE
    Identification of direct targets of FUSCA3, a key regulator of Arabidopsis seed development.
    Plant Physiol., 2013. 161(3): p. 1251-64
    [PMID:23314941]
  15. Efroni I, et al.
    Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses.
    Dev. Cell, 2013. 24(4): p. 438-45
    [PMID:23449474]
  16. Li-Beisson Y, et al.
    Acyl-lipid metabolism.
    Arabidopsis Book, 2013. 11: p. e0161
    [PMID:23505340]
  17. Jia H,McCarty DR,Suzuki M
    Distinct roles of LAFL network genes in promoting the embryonic seedling fate in the absence of VAL repression.
    Plant Physiol., 2013. 163(3): p. 1293-305
    [PMID:24043445]
  18. Sharma N,Bender Y,Boyle K,Fobert PR
    High-level expression of sugar inducible gene2 (HSI2) is a negative regulator of drought stress tolerance in Arabidopsis.
    BMC Plant Biol., 2013. 13: p. 170
    [PMID:24168327]
  19. Veerappan V,Chen N,Reichert AI,Allen RD
    HSI2/VAL1 PHD-like domain promotes H3K27 trimethylation to repress the expression of seed maturation genes and complex transgenes in Arabidopsis seedlings.
    BMC Plant Biol., 2014. 14: p. 293
    [PMID:25367506]
  20. Schneider A, et al.
    Potential targets of VIVIPAROUS1/ABI3-LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos.
    Plant J., 2016. 85(2): p. 305-19
    [PMID:26678037]
  21. Chhun T, et al.
    HSI2 Repressor Recruits MED13 and HDA6 to Down-Regulate Seed Maturation Gene Expression Directly During Arabidopsis Early Seedling Growth.
    Plant Cell Physiol., 2016. 57(8): p. 1689-706
    [PMID:27335347]
  22. Qüesta JI,Song J,Geraldo N,An H,Dean C
    Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization.
    Science, 2016. 353(6298): p. 485-8
    [PMID:27471304]
  23. Yuan W, et al.
    A cis cold memory element and a trans epigenome reader mediate Polycomb silencing of FLC by vernalization in Arabidopsis.
    Nat. Genet., 2016. 48(12): p. 1527-1534
    [PMID:27819666]
  24. Merini W, et al.
    The Arabidopsis Polycomb Repressive Complex 1 (PRC1) Components AtBMI1A, B, and C Impact Gene Networks throughout All Stages of Plant Development.
    Plant Physiol., 2017. 173(1): p. 627-641
    [PMID:27837089]
  25. Li C,Cui Y
    A DNA element that remembers winter.
    Nat. Genet., 2016. 48(12): p. 1451-1452
    [PMID:27898079]
  26. Chen N,Veerappan V,Abdelmageed H,Kang M,Allen RD
    HSI2/VAL1 Silences AGL15 to Regulate the Developmental Transition from Seed Maturation to Vegetative Growth in Arabidopsis.
    Plant Cell, 2018. 30(3): p. 600-619
    [PMID:29475938]
  27. Sasnauskas G,Kauneckaite K,Siksnys V
    Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1.
    Nucleic Acids Res., 2018. 46(8): p. 4316-4324
    [PMID:29660015]
  28. Wu B, et al.
    Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana.
    Biochem. Biophys. Res. Commun., 2018. 501(2): p. 415-422
    [PMID:29733847]