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Protein

Protein SHORT-ROOT

Gene

SHR

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Transcription factor required for quiescent center cells specification and maintenance of surrounding stem cells, and for the asymmetric cell division involved in radial pattern formation in roots. Essential for both cell division and cell specification. Regulates the radial organization of the shoot axial organs and is required for normal shoot gravitropism. Directly controls the transcription of SCR, and when associated with SCR, of MGP, RLK, TRI, NUC and SCL3.6 Publications

GO - Molecular functioni

  1. sequence-specific DNA binding Source: TAIR
  2. sequence-specific DNA binding transcription factor activity Source: TAIR

GO - Biological processi

  1. asymmetric cell division Source: TAIR
  2. iron ion homeostasis Source: TAIR
  3. leaf development Source: TAIR
  4. negative regulation of mitotic cell cycle Source: TAIR
  5. radial pattern formation Source: TAIR
  6. regulation of hormone metabolic process Source: TAIR
  7. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Transcription, Transcription regulation

Names & Taxonomyi

Protein namesi
Recommended name:
Protein SHORT-ROOT
Short name:
AtSHR
Alternative name(s):
GRAS family protein 26
Short name:
AtGRAS-26
Protein SHOOT GRAVITROPISM 7
Gene namesi
Name:SHR
Synonyms:SGR7
Ordered Locus Names:At4g37650
ORF Names:F19F18.140
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G37650.

Subcellular locationi

  1. Cytoplasm 3 Publications
  2. Nucleus 3 Publications
  3. Early endosome 1 Publication
  4. Late endosome 1 Publication
  5. Recycling endosome 1 Publication

  6. Note: Cytoplasm and nucleus in the stele (PubMed:11565032, PubMed:15498493). Restricted to the nucleus in adjacent cells (PubMed:11565032, PubMed:15498493). Localization to endosomes promotes the intercellular movement of SHR (PubMed:25124761).3 Publications

GO - Cellular componenti

  1. early endosome Source: UniProtKB-SubCell
  2. late endosome Source: UniProtKB-SubCell
  3. nucleus Source: TAIR
  4. recycling endosome Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endosome, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi289 – 2891T → I or E: Loss of both export from the stele and activity. 1 Publication
Mutagenesisi342 – 3476LNELDV → AAA: No effect on activity, but loss of movment into the endodermis and reduction in the nuclear localization in the stele. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 531531Protein SHORT-ROOTPRO_0000329423Add
BLAST

Proteomic databases

PaxDbiQ9SZF7.
PRIDEiQ9SZF7.

Expressioni

Tissue specificityi

Expressed in the stele and the quiescent center. Not detected in the ground tissue cell lineage. The SHR protein moves from the stele to a single layer of adjacent cells, where it enters the nucleus.4 Publications

Developmental stagei

Expressed in the procambium during embryogenesis.1 Publication

Gene expression databases

GenevestigatoriQ9SZF7.

Interactioni

Subunit structurei

Interacts with SCR, SCL23, JKD and MGP (PubMed:16640459, PubMed:17446396, PubMed:17785527, PubMed:18500650). Interacts with SIEL (PubMed:21924907). Association to endosomes and intercellular movement of SHR rely on the interaction with SIEL (PubMed:25124761).6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
SCRQ9M38411EBI-1250472,EBI-1250484

Protein-protein interaction databases

BioGridi15200. 1 interaction.
IntActiQ9SZF7. 6 interactions.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi256 – 2605VHIID

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi11 – 155Poly-Gln
Compositional biasi29 – 346Poly-Thr
Compositional biasi65 – 695Poly-Ser
Compositional biasi70 – 767His-rich
Compositional biasi104 – 1107Poly-Ala

Sequence similaritiesi

Belongs to the GRAS family.Curated

Phylogenomic databases

eggNOGiNOG301144.
HOGENOMiHOG000078767.
InParanoidiQ9SZF7.
OMAiSSHHTHN.
PhylomeDBiQ9SZF7.

Family and domain databases

InterProiIPR030019. Short-root.
IPR005202. TF_GRAS.
[Graphical view]
PANTHERiPTHR31636:SF9. PTHR31636:SF9. 1 hit.
PfamiPF03514. GRAS. 1 hit.
[Graphical view]
PROSITEiPS50985. GRAS. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9SZF7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDTLFRLVSL QQQQQSDSII TNQSSLSRTS TTTTGSPQTA YHYNFPQNDV
60 70 80 90 100
VEECFNFFMD EEDLSSSSSH HNHHNHNNPN TYYSPFTTPT QYHPATSSTP
110 120 130 140 150
SSTAAAAALA SPYSSSGHHN DPSAFSIPQT PPSFDFSANA KWADSVLLEA
160 170 180 190 200
ARAFSDKDTA RAQQILWTLN ELSSPYGDTE QKLASYFLQA LFNRMTGSGE
210 220 230 240 250
RCYRTMVTAA ATEKTCSFES TRKTVLKFQE VSPWATFGHV AANGAILEAV
260 270 280 290 300
DGEAKIHIVD ISSTFCTQWP TLLEALATRS DDTPHLRLTT VVVANKFVND
310 320 330 340 350
QTASHRMMKE IGNRMEKFAR LMGVPFKFNI IHHVGDLSEF DLNELDVKPD
360 370 380 390 400
EVLAINCVGA MHGIASRGSP RDAVISSFRR LRPRIVTVVE EEADLVGEEE
410 420 430 440 450
GGFDDEFLRG FGECLRWFRV CFESWEESFP RTSNERLMLE RAAGRAIVDL
460 470 480 490 500
VACEPSDSTE RRETARKWSR RMRNSGFGAV GYSDEVADDV RALLRRYKEG
510 520 530
VWSMVQCPDA AGIFLCWRDQ PVVWASAWRP T
Length:531
Mass (Da):59,462
Last modified:May 1, 2000 - v1
Checksum:iF43EEC5F7AA0CA1C
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti233 – 2331P → S in AAL69513 (Ref. 4) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF233752 Genomic DNA. Translation: AAF75234.1.
AL035605 Genomic DNA. Translation: CAB38304.1.
AL161591 Genomic DNA. Translation: CAB80430.1.
CP002687 Genomic DNA. Translation: AEE86820.1.
BT033026 mRNA. Translation: ACE62894.1.
AY074547 mRNA. Translation: AAL69513.1.
PIRiT04722.
RefSeqiNP_195480.1. NM_119928.2.
UniGeneiAt.2816.
At.71893.

Genome annotation databases

EnsemblPlantsiAT4G37650.1; AT4G37650.1; AT4G37650.
GeneIDi829919.
KEGGiath:AT4G37650.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF233752 Genomic DNA. Translation: AAF75234.1.
AL035605 Genomic DNA. Translation: CAB38304.1.
AL161591 Genomic DNA. Translation: CAB80430.1.
CP002687 Genomic DNA. Translation: AEE86820.1.
BT033026 mRNA. Translation: ACE62894.1.
AY074547 mRNA. Translation: AAL69513.1.
PIRiT04722.
RefSeqiNP_195480.1. NM_119928.2.
UniGeneiAt.2816.
At.71893.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi15200. 1 interaction.
IntActiQ9SZF7. 6 interactions.

Proteomic databases

PaxDbiQ9SZF7.
PRIDEiQ9SZF7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G37650.1; AT4G37650.1; AT4G37650.
GeneIDi829919.
KEGGiath:AT4G37650.

Organism-specific databases

GeneFarmi4260. 427.
TAIRiAT4G37650.

Phylogenomic databases

eggNOGiNOG301144.
HOGENOMiHOG000078767.
InParanoidiQ9SZF7.
OMAiSSHHTHN.
PhylomeDBiQ9SZF7.

Miscellaneous databases

PROiQ9SZF7.

Gene expression databases

GenevestigatoriQ9SZF7.

Family and domain databases

InterProiIPR030019. Short-root.
IPR005202. TF_GRAS.
[Graphical view]
PANTHERiPTHR31636:SF9. PTHR31636:SF9. 1 hit.
PfamiPF03514. GRAS. 1 hit.
[Graphical view]
PROSITEiPS50985. GRAS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling."
    Helariutta Y., Fukaki H., Wysocka-Diller J.W., Nakajima K., Jung J., Sena G., Hauser M.-T., Benfey P.N.
    Cell 101:555-567(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
  2. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
    Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
    , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
    Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Arabidopsis ORF clones."
    De Los Reyes C., Quan R., Chen H., Bautista V.R., Kim C.J., Ecker J.R.
    Submitted (JUN-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 54-531.
    Strain: cv. Columbia.
  6. "Genetic evidence that the endodermis is essential for shoot gravitropism in Arabidopsis thaliana."
    Fukaki H., Wysocka-Diller J.W., Kato T., Fujisawa H., Benfey P.N., Tasaka M.
    Plant J. 14:425-430(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION, FUNCTION.
  7. "Intercellular movement of the putative transcription factor SHR in root patterning."
    Nakajima K., Sena G., Nawy T., Benfey P.N.
    Nature 413:307-311(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, SUBCELLULAR LOCATION, TRANSLOCATION.
  8. "SCARECROW is involved in positioning the stem cell niche in the Arabidopsis root meristem."
    Sabatini S., Heidstra R., Wildwater M., Scheres B.
    Genes Dev. 17:354-358(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "Mosaic analyses using marked activation and deletion clones dissect Arabidopsis SCARECROW action in asymmetric cell division."
    Heidstra R., Welch D., Scheres B.
    Genes Dev. 18:1964-1969(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY.
  10. "A broad competence to respond to SHORT ROOT revealed by tissue-specific ectopic expression."
    Sena G., Jung J.W., Benfey P.N.
    Development 131:2817-2826(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, TRANSLOCATION.
  11. "Mechanisms regulating SHORT-ROOT intercellular movement."
    Gallagher K.L., Paquette A.J., Nakajima K., Benfey P.N.
    Curr. Biol. 14:1847-1851(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, MUTAGENESIS OF THR-289.
  12. Cited for: FUNCTION, INTERACTION WITH SCR.
  13. "An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants."
    Cui H., Levesque M.P., Vernoux T., Jung J.W., Paquette A.J., Gallagher K.L., Wang J.Y., Blilou I., Scheres B., Benfey P.N.
    Science 316:421-425(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH SCR.
  14. "Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit asymmetric cell division and stabilize tissue boundaries by restricting SHORT-ROOT action."
    Welch D., Hassan H., Blilou I., Immink R., Heidstra R., Scheres B.
    Genes Dev. 21:2196-2204(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH JKD AND MGP.
  15. Cited for: INTERACTION WITH SCR AND SCL23.
  16. "Both the conserved GRAS domain and nuclear localization are required for SHORT-ROOT movement."
    Gallagher K.L., Benfey P.N.
    Plant J. 57:785-797(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF 342-LEU--VAL-347, MISCELLANEOUS.
  17. "An essential protein that interacts with endosomes and promotes movement of the SHORT-ROOT transcription factor."
    Koizumi K., Wu S., MacRae-Crerar A., Gallagher K.L.
    Curr. Biol. 21:1559-1564(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH SIEL, MISCELLANEOUS.
  18. "Intact microtubules are required for the intercellular movement of the SHORT-ROOT transcription factor."
    Wu S., Gallagher K.L.
    Plant J. 74:148-159(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: MISCELLANEOUS.
  19. "The movement of the non-cell-autonomous transcription factor, SHORT-ROOT relies on the endomembrane system."
    Wu S., Gallagher K.L.
    Plant J. 80:396-409(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.

Entry informationi

Entry nameiSHR_ARATH
AccessioniPrimary (citable) accession number: Q9SZF7
Secondary accession number(s): B3DNN8, Q8RU28
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 8, 2008
Last sequence update: May 1, 2000
Last modified: April 29, 2015
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

Moves via plasmodesmata from the stele into the adjacent cell layer where it locates in the nucleus to controls SCR transcription and endodermis specification. Intact microtubules are required for cell-to-cell trafficking of SHR (PubMed:23294290). This intercellular movement is dependent upon the endosome localized protein SIEL (PubMed:21924907). It is necessary for normal patterning of the root (PubMed:19000160).3 Publications

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.