PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

AT3G54220.1

Common Name

F24B22.180, SCR, SGR1

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

GRAS

Protein Properties

Length: 653aa MW: 71505.6 Da PI: 6.1714

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G54220.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	426.6	2e-130	291	650	2	374
GRAS 2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshltaN 99 +lLl+cAeavs+++le+a++lL ++s+l++p+g++ qR+aayf eA++arl++s+ ++y+alp++ ++++s + ++a+++f+ +sP++kfsh+taN AT3G54220.1 291 LTLLLQCAEAVSADNLEEANKLLLEISQLSTPYGTSAQRVAAYFSEAMSARLLNSCLGIYAALPSRWMPQTHSLKMVSAFQVFNGISPLVKFSHFTAN 388 579********************************************************************************************* PP GRAS 100 qaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledleleeLrvk 197 qaI ea+e+e+ vHiiD+di+qGlQWp L++ LasRp+gpp++R+Tg+g s e+l++tg+rL++fA++lg+pfef + +a+++ +l++e+L+v+ AT3G54220.1 389 QAIQEAFEKEDSVHIIDLDIMQGLQWPGLFHILASRPGGPPHVRLTGLGT----SMEALQATGKRLSDFADKLGLPFEFCP-LAEKVGNLDTERLNVR 481 **********************************************....***********************.59********** PP GRAS 198 pgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgreiv 295 ++Ea+aV++ h+l+d ++s ++ +L+l+++l Pkvv+vveq+++h ++sFl rf+ea++yysalfdsl a++++eseer++vE++ll++ei+ AT3G54220.1 482 KREAVAVHWLQ--HSLYDVTGSDAH----TLWLLQRLAPKVVTVVEQDLSH-AGSFLGRFVEAIHYYSALFDSLGASYGEESEERHVVEQQLLSKEIR 572 ******9..999988888888....******************.899*************************************** PP GRAS 296 nvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 nv+a g +r + + +e+Wre+++++GFk ++l +aa+qa lll +++sdgy++ +++g+l lgWkd +L+++SaW+ AT3G54220.1 573 NVLAVGGPSRSGEVK-FESWREKMQQCGFKGISLAGNAATQATLLLGMFPSDGYTLVDDNGTLKLGWKDLSLLTASAWT 650 *****888776.************************************************************6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	61.686	264	630	IPR005202	Transcription factor GRAS
Pfam	PF03514	6.8E-128	291	650	IPR005202	Transcription factor GRAS

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0008356	Biological Process	asymmetric cell division
GO:0009630	Biological Process	gravitropism
GO:0009956	Biological Process	radial pattern formation
GO:0048366	Biological Process	leaf development
GO:0051457	Biological Process	maintenance of protein location in nucleus
GO:0090610	Biological Process	bundle sheath cell fate specification
GO:0005634	Cellular Component	nucleus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding
GO:0043565	Molecular Function	sequence-specific DNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0005059	anatomy	root endodermis
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020149	anatomy	quiescent center
PO:0025022	anatomy	collective leaf structure
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 653 aa Download sequence Send to blast
MAESGDFNGG QPPPHSPLRT TSSGSSSSNN RGPPPPPPPP LVMVRKRLAS EMSSNPDYNN 60 SSRPPRRVSH LLDSNYNTVT PQQPPSLTAA ATVSSQPNPP LSVCGFSGLP VFPSDRGGRN 120 VMMSVQPMDQ DSSSSSASPT VWVDAIIRDL IHSSTSVSIP QLIQNVRDII FPCNPNLGAL 180 LEYRLRSLML LDPSSSSDPS PQTFEPLYQI SNNPSPPQQQ QQHQQQQQQH KPPPPPIQQQ 240 ERENSSTDAP PQPETVTATV PAVQTNTAEA LRERKEEIKR QKQDEEGLHL LTLLLQCAEA 300 VSADNLEEAN KLLLEISQLS TPYGTSAQRV AAYFSEAMSA RLLNSCLGIY AALPSRWMPQ 360 THSLKMVSAF QVFNGISPLV KFSHFTANQA IQEAFEKEDS VHIIDLDIMQ GLQWPGLFHI 420 LASRPGGPPH VRLTGLGTSM EALQATGKRL SDFADKLGLP FEFCPLAEKV GNLDTERLNV 480 RKREAVAVHW LQHSLYDVTG SDAHTLWLLQ RLAPKVVTVV EQDLSHAGSF LGRFVEAIHY 540 YSALFDSLGA SYGEESEERH VVEQQLLSKE IRNVLAVGGP SRSGEVKFES WREKMQQCGF 600 KGISLAGNAA TQATLLLGMF PSDGYTLVDD NGTLKLGWKD LSLLTASAWT PRS

Sequence ? help Back to Top

Protein Sequence Length: 653 aa Download sequence Send to blast

MAESGDFNGG QPPPHSPLRT TSSGSSSSNN RGPPPPPPPP LVMVRKRLAS EMSSNPDYNN  60
SSRPPRRVSH LLDSNYNTVT PQQPPSLTAA ATVSSQPNPP LSVCGFSGLP VFPSDRGGRN  120
VMMSVQPMDQ DSSSSSASPT VWVDAIIRDL IHSSTSVSIP QLIQNVRDII FPCNPNLGAL  180
LEYRLRSLML LDPSSSSDPS PQTFEPLYQI SNNPSPPQQQ QQHQQQQQQH KPPPPPIQQQ  240
ERENSSTDAP PQPETVTATV PAVQTNTAEA LRERKEEIKR QKQDEEGLHL LTLLLQCAEA  300
VSADNLEEAN KLLLEISQLS TPYGTSAQRV AAYFSEAMSA RLLNSCLGIY AALPSRWMPQ  360
THSLKMVSAF QVFNGISPLV KFSHFTANQA IQEAFEKEDS VHIIDLDIMQ GLQWPGLFHI  420
LASRPGGPPH VRLTGLGTSM EALQATGKRL SDFADKLGLP FEFCPLAEKV GNLDTERLNV  480
RKREAVAVHW LQHSLYDVTG SDAHTLWLLQ RLAPKVVTVV EQDLSHAGSF LGRFVEAIHY  540
YSALFDSLGA SYGEESEERH VVEQQLLSKE IRNVLAVGGP SRSGEVKFES WREKMQQCGF  600
KGISLAGNAA TQATLLLGMF PSDGYTLVDD NGTLKLGWKD LSLLTASAWT PRS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	0.0	274	653	3	382	Protein SCARECROW
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.932	0.0	floral meristem\| flower\| root\| vegetative tissue

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	42565917	0.0
Genevisible	251890_at	0.0
Expression Atlas	AT3G54220	-
AtGenExpress	AT3G54220	-
ATTED-II	AT3G54220	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Detected in the ground tissue of late heart-stage embryos. After germination, expressed also in the L1 layer throughout the shoot apical meristem including the peripheral zone. Detected in most tissues of young leaf primordia, except in the presumptive vasculature. In mature leaves, expressed in bundle sheath cells. Detected in inflorescence stems in a single internal cell layer corresponding to the starch sheath. {ECO:0000269\|PubMed:10631180, ECO:0000269\|PubMed:8756724}.
Uniprot	TISSUE SPECIFICITY: Expressed in siliques, leaves and roots. Detected in the initial daughter cell before its asymmetric division and remains expressed only in the endodermal cell layer after the division. Expressed in the endodermis or starch sheath of the seedling hypocotyl, in the leaf bundle sheath cells and the root quiescent center. {ECO:0000269\|PubMed:10631180, ECO:0000269\|PubMed:10850497, ECO:0000269\|PubMed:11565032, ECO:0000269\|PubMed:8756724, ECO:0000269\|PubMed:9375406}.

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a member of a novel family having similarity to DNA binding proteins containing basic-leucine zipper regions; scr is expressed in cortex/endodermal initial cells and in the endodermal cell lineage. Regulates the radial organization of the root. Is required cell-autonomously for distal specification of the quiescent center, which in turn regulates stem cell fate of immediately surrounding cells. SCR appears to be a direct target of SHR.
UniProt	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 cell division but not differentiation of the ground tissue. Also required for normal shoot gravitropism. Regulates the radial organization of the shoot axial organs. Binds to the promoter of MGP, NUC, RLK and SCL3. Restricts SHR movment and sequesters it into the nucleus of the endodermis. {ECO:0000269\|PubMed:10631180, ECO:0000269\|PubMed:12569126, ECO:0000269\|PubMed:15142972, ECO:0000269\|PubMed:15314023, ECO:0000269\|PubMed:16640459, ECO:0000269\|PubMed:17446396, ECO:0000269\|PubMed:22921914, ECO:0000269\|PubMed:24302889, ECO:0000269\|PubMed:8819871, ECO:0000269\|PubMed:9375406, ECO:0000269\|PubMed:9670559}.

Function -- GeneRIF ? help Back to Top
findings show that SCARECROW (SCR) blocks SHORTROOT (SHR) movement by sequestering it into the nucleus through protein-protein interaction and a safeguard mechanism that relies on a SHR/SCR-dependent positive feedback loop for SCR transcription [PMID: 17446396] LHP1 acts together with SCR to suppress premature middle cortex formation. [PMID: 19228333] SHR and SCR primarily function as general regulators of cell proliferation in leaves. [PMID: 20739610] Studies indicate that GRAS proteins are named after the first three members: GIBBERELLIC ACID INSENSITIVE (GAI), REPRESSOR of GAI (RGA) and SCARECROW (SCR), and they have diverse roles in plant development and signal transduction. [PMID: 21732203] The MKO1 gene plays an important role in the maintenance of the root apical meristem proliferative capacity and indeterminate root growth, which apparently acts independently of the SCR/SHR and WOX5 regulatory pathways. [PMID: 21744091] JKD directly regulates SCR and MGP expression in cooperation with SHR, SCR and MGP. [PMID: 21935722] SHR and SCR regulate a similar but not identical set of stress response genes. [PMID: 22312006] Study tissue-generating asymmetric divisions in a stem cell daughter within the Arabidopsis root finds spatial restriction of these divisions requires physical binding of the stem cell regulator SCARECROW (SCR) by the RETINOBLASTOMA-RELATED (RBR) protein. [PMID: 22921914] SCARECROW reinforces SHORT-ROOT signaling and inhibits periclinal cell divisions in the ground tissue by maintaining SHR at high levels in the endodermis. [PMID: 23072993] SHRUBBY (At5g24740) controls root growth downstream of gibberellic acid in part through the regulation of SHORT-ROOT and SCARECROW. [PMID: 23444357] A defect in SGR1 leads to leaf stay-green phenotypes in Arabidopsis and rice. [PMID: 24043799] RBR interacts with the stem cell transcription factor SCARECROW (SCR) through an LxCxE motif. [PMID: 24302889] Mutations in three GRAS family transcription factors, SHORT-ROOT (SHR), SCARECROW (SCR) and SCARECROW-LIKE 23 (SCL23), affect BS cell fate in Arabidopsis thaliana. [PMID: 24517883] These results suggest that endogenous L-cysteine level acts to maintain root stem cell niche by regulating basal- and auxin-induced expression of PLT1/2 and SCR/SHR. [PMID: 24798139] Arabidopsis adventitious root formation and xylogenesis are developmental programmes that are inversely related, but they involve fine-tuning by the same proteins, namely SHR, SCR and AUX1. [PMID: 25617411] Data show that SCARECROW-LIKE23 (SCL23) is a mobile protein that controls movement of SHORT-ROOT (SHR) and acts redundantly with SCARCROW (SCR) to specify endodermal fate in the root meristem. [PMID: 26415082] Data indicate that SEUSS (SEU) gene has distinct genetic interactions with SHORT-ROOT (SHR), SCARECROW (SCR), and SCARECROW-LIKE3 (SCL3) genes. [PMID: 26818732] SCARECROW controls Arabidopsis root meristem size from the root endodermis tissue by regulating the DELLA protein RGA that in turn mediates the regulation of ARR1 levels at the transition zone. [PMID: 26848984] results provide new insights into the regulatory role of the SHR-SCR-SCL23 network in the endodermis development in both roots and shoots. [PMID: 27353361] The photorespiratory phenotype of cat2-2 mutants did not depend on the SHR functional interactor SCARECROW and the sugar signaling component ABSCISIC ACID INSENSITIVE4, despite the requirement for exogenous sucrose for cell death attenuation in cat2-2 shr-6 double mutants. [PMID: 27432873] QC precursor cells originated from the outer layer of stage II lateral root primordia, within which the SCARECROW (SCR) transcription factor was specifically expressed. Disrupting SCR function abolished periclinal divisions in this lateral root primordia cell layer and perturbed the formation of QC precursor cells. [PMID: 27510971] modeling, transcriptional reporters, and synthetic promoters support a mechanism whereby expression at the top of the SHORTROOT-SCARECROW cascade is established through opposing activities of activators and repressors [PMID: 27923776] In the crystal structures of the SHR-SCR binary and JACKDAW (JKD)/IDD10-SHR-SCR ternary complexes, each GRAS domain comprises one alpha/beta core subdomain with an alpha-helical cap that mediates heterodimerization by forming an intermolecular helix bundle. [PMID: 28211915] This study showed that INDETERMINATE DOMAIN PROTEIN (ID) binding sequences have a crucial role in the regulation of SCARECROW and SHORT-ROOT expression.[SCARECROW] [PMID: 28324206] This study showed that INDETERMINATE DOMAIN PROTEIN binding sequences have a crucial role in the regulation of SCARECROW and SHORT-ROOT expression. [PMID: 28324206] SCR and PLETHORA genetically and physically interact with plant-specific teosinte-branched cycloidea PCNA (TCP) transcription factors to specify the stem cell niche during embryogenesis and maintain organizer cells post-embryonically. [PMID: 30018102]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT3G54220.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated by SHR and by itself. {ECO:0000269\|PubMed:10850497, ECO:0000269\|PubMed:11565032, ECO:0000269\|PubMed:15314023}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT4G37650 (A), AT5G03150 (A)

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT1G03840(A), AT3G12280(A), AT5G03150(A)

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT4G37650
IntAct	Search Q9M384

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION PHENOTYPE: Plants have a greatly reduced root length and only a single cell layer between the epidermis and the pericycle. The sgrl-1 mutant has no gravitropic response either in inflorescence stems or in hypocotyls. {ECO:0000269\|PubMed:10631180, ECO:0000269\|PubMed:8756724, ECO:0000269\|PubMed:8819871, ECO:0000269\|PubMed:9670559}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G54220

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY056315	0.0	AY056315.1 Arabidopsis thaliana putative SCARECROW1 protein (At3g54220) mRNA, complete cds.
GenBank	AY080840	0.0	AY080840.1 Arabidopsis thaliana putative SCARECROW1 protein (At3g54220) mRNA, complete cds.
GenBank	AY113991	0.0	AY113991.1 Arabidopsis thaliana putative SCARECROW1 protein (At3g54220) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_190990.1	0.0	GRAS family transcription factor
Swissprot	Q9M384	0.0	SCR_ARATH; Protein SCARECROW
TrEMBL	A0A178V8F9	0.0	A0A178V8F9_ARATH; SGR1
STRING	AT3G54220.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM8164	26	40
Representative plant	OGRP2183	14	37

Link Out ? help Back to Top
Phytozome	AT3G54220.1
Entrez Gene	824589
iHOP	AT3G54220
wikigenes	AT3G54220

Publications ? help Back to Top
Tasaka M,Kato T,Fukaki H The endodermis and shoot gravitropism Trends Plant Sci., 1999. 4(3): p. 103-7 [PMID:10322541] Liu YG, et al. Complementation of plant mutants with large genomic DNA fragments by a transformation-competent artificial chromosome vector accelerates positional cloning. Proc. Natl. Acad. Sci. U.S.A., 1999. 96(11): p. 6535-40 [PMID:10339623] Pysh LD,Wysocka-Diller JW,Camilleri C,Bouchez D,Benfey PN The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes. Plant J., 1999. 18(1): p. 111-9 [PMID:10341448] Wysocka-Diller JW,Helariutta Y,Fukaki H,Malamy JE,Benfey PN Molecular analysis of SCARECROW function reveals a radial patterning mechanism common to root and shoot. Development, 2000. 127(3): p. 595-603 [PMID:10631180] Helariutta Y, et al. The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling. Cell, 2000. 101(5): p. 555-67 [PMID:10850497] Lim J, et al. Molecular analysis of the SCARECROW gene in maize reveals a common basis for radial patterning in diverse meristems. Plant Cell, 2000. 12(8): p. 1307-18 [PMID:10948251] Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Kaya H, et al. FASCIATA genes for chromatin assembly factor-1 in arabidopsis maintain the cellular organization of apical meristems. Cell, 2001. 104(1): p. 131-42 [PMID:11163246] Sassa N,Matsushita Y,Nakamura T,Nyunoya H The molecular characterization and in situ expression pattern of pea SCARECROW gene. Plant Cell Physiol., 2001. 42(4): p. 385-94 [PMID:11333309] Nakajima K,Sena G,Nawy T,Benfey PN Intercellular movement of the putative transcription factor SHR in root patterning. Nature, 2001. 413(6853): p. 307-11 [PMID:11565032] Barton MK Giving meaning to movement. Cell, 2001. 107(2): p. 129-32 [PMID:11672520] Morita MT, et al. Involvement of the vacuoles of the endodermis in the early process of shoot gravitropism in Arabidopsis. Plant Cell, 2002. 14(1): p. 47-56 [PMID:11826298] Kato T,Morita MT,Tasaka M Role of endodermal cell vacuoles in shoot gravitropism. J. Plant Growth Regul., 2002. 21(2): p. 113-9 [PMID:12024223] Long JA,Woody S,Poethig S,Meyerowitz EM,Barton MK Transformation of shoots into roots in Arabidopsis embryos mutant at the TOPLESS locus. Development, 2002. 129(12): p. 2797-806 [PMID:12050130] Mylona P,Linstead P,Martienssen R,Dolan L SCHIZORIZA controls an asymmetric cell division and restricts epidermal identity in the Arabidopsis root. Development, 2002. 129(18): p. 4327-34 [PMID:12183384] Charrier B,Champion A,Henry Y,Kreis M Expression profiling of the whole Arabidopsis shaggy-like kinase multigene family by real-time reverse transcriptase-polymerase chain reaction. Plant Physiol., 2002. 130(2): p. 577-90 [PMID:12376626] Stasolla C, et al. The effects of polyethylene glycol on gene expression of developing white spruce somatic embryos. Plant Physiol., 2003. 131(1): p. 49-60 [PMID:12529514] Sabatini S,Heidstra R,Wildwater M,Scheres B SCARECROW is involved in positioning the stem cell niche in the Arabidopsis root meristem. Genes Dev., 2003. 17(3): p. 354-8 [PMID:12569126] Day RB,Shibuya N,Minami E Identification and characterization of two new members of the GRAS gene family in rice responsive to N-acetylchitooligosaccharide elicitor. Biochim. Biophys. Acta, 2003. 1625(3): p. 261-8 [PMID:12591613] Grube RC,Brennan EB,Ryder EJ Characterization and genetic analysis of a lettuce (Lactuca sativa L.) mutant, weary, that exhibits reduced gravitropic response in hypocotyls and inflorescence stems. J. Exp. Bot., 2003. 54(385): p. 1259-68 [PMID:12654877] Boutet S, et al. Arabidopsis HEN1: a genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance. Curr. Biol., 2003. 13(10): p. 843-8 [PMID:12747833] Yano D, et al. A SNARE complex containing SGR3/AtVAM3 and ZIG/VTI11 in gravity-sensing cells is important for Arabidopsis shoot gravitropism. Proc. Natl. Acad. Sci. U.S.A., 2003. 100(14): p. 8589-94 [PMID:12815100] Kamiya N,Itoh J,Morikami A,Nagato Y,Matsuoka M The SCARECROW gene's role in asymmetric cell divisions in rice plants. Plant J., 2003. 36(1): p. 45-54 [PMID:12974810] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] J Growing up green: cellular basis of plant development. Mech. Dev., 2003. 120(11): p. 1395-406 [PMID:14623445] Soga K,Wakabayashi K,Kamisaka S,Hoson T Graviperception in growth inhibition of plant shoots under hypergravity conditions produced by centrifugation is independent of that in gravitropism and may involve mechanoreceptors. Planta, 2004. 218(6): p. 1054-61 [PMID:14716566] Bolle C The role of GRAS proteins in plant signal transduction and development. Planta, 2004. 218(5): p. 683-92 [PMID:14760535] Suzuki T, et al. A novel Arabidopsis gene TONSOKU is required for proper cell arrangement in root and shoot apical meristems. Plant J., 2004. 38(4): p. 673-84 [PMID:15125773] Sena G,Jung JW,Benfey PN A broad competence to respond to SHORT ROOT revealed by tissue-specific ectopic expression. Development, 2004. 131(12): p. 2817-26 [PMID:15142972] Heidstra R,Welch D,Scheres B Mosaic analyses using marked activation and deletion clones dissect Arabidopsis SCARECROW action in asymmetric cell division. Genes Dev., 2004. 18(16): p. 1964-9 [PMID:15314023] Aida M, et al. The PLETHORA genes mediate patterning of the Arabidopsis root stem cell niche. Cell, 2004. 119(1): p. 109-20 [PMID:15454085] Montiel G,Gantet P,Jay-Allemand C,Breton C Transcription factor networks. Pathways to the knowledge of root development. Plant Physiol., 2004. 136(3): p. 3478-85 [PMID:15542499] Paquette AJ,Benfey PN Maturation of the ground tissue of the root is regulated by gibberellin and SCARECROW and requires SHORT-ROOT. Plant Physiol., 2005. 138(2): p. 636-40 [PMID:15955927] Fukaki H,Nakao Y,Okushima Y,Theologis A,Tasaka M Tissue-specific expression of stabilized SOLITARY-ROOT/IAA14 alters lateral root development in Arabidopsis. Plant J., 2005. 44(3): p. 382-95 [PMID:16236149] Kitazawa D, et al. Shoot circumnutation and winding movements require gravisensing cells. Proc. Natl. Acad. Sci. U.S.A., 2005. 102(51): p. 18742-7 [PMID:16339910] Wildwater M, et al. The RETINOBLASTOMA-RELATED gene regulates stem cell maintenance in Arabidopsis roots. Cell, 2005. 123(7): p. 1337-49 [PMID:16377572] Xu J, et al. A molecular framework for plant regeneration. Science, 2006. 311(5759): p. 385-8 [PMID:16424342] Levesque MP, et al. Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol., 2006. 4(5): p. e143 [PMID:16640459] Morita MT, et al. A C2H2-type zinc finger protein, SGR5, is involved in early events of gravitropism in Arabidopsis inflorescence stems. Plant J., 2006. 47(4): p. 619-28 [PMID:16813575] Imin N,Nizamidin M,Wu T,Rolfe BG Factors involved in root formation in Medicago truncatula. J. Exp. Bot., 2007. 58(3): p. 439-51 [PMID:17158109] Dello Ioio R, et al. Cytokinins determine Arabidopsis root-meristem size by controlling cell differentiation. Curr. Biol., 2007. 17(8): p. 678-82 [PMID:17363254] K A method for cellular localization of gene expression via quantitative in situ hybridization in plants. Plant J., 2007. 50(1): p. 159-75 [PMID:17397510] Cui H, et al. An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. Science, 2007. 316(5823): p. 421-5 [PMID:17446396] Ortega-Mart Ethylene modulates stem cell division in the Arabidopsis thaliana root. Science, 2007. 317(5837): p. 507-10 [PMID:17656722] Welch D, et al. Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit asymmetric cell division and stabilize tissue boundaries by restricting SHORT-ROOT action. Genes Dev., 2007. 21(17): p. 2196-204 [PMID:17785527] Zentella R, et al. Global analysis of della direct targets in early gibberellin signaling in Arabidopsis. Plant Cell, 2007. 19(10): p. 3037-57 [PMID:17933900] Ten Hove CA,Heidstra R Who begets whom? Plant cell fate determination by asymmetric cell division. Curr. Opin. Plant Biol., 2008. 11(1): p. 34-41 [PMID:18162432] Saiga S, et al. The Arabidopsis OBERON1 and OBERON2 genes encode plant homeodomain finger proteins and are required for apical meristem maintenance. Development, 2008. 135(10): p. 1751-9 [PMID:18403411] Dinneny JR, et al. Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science, 2008. 320(5878): p. 942-5 [PMID:18436742] Lee MH, et al. Large-scale analysis of the GRAS gene family in Arabidopsis thaliana. Plant Mol. Biol., 2008. 67(6): p. 659-70 [PMID:18500650] Iyer-Pascuzzi AS,Benfey PN Transcriptional networks in root cell fate specification. Biochim. Biophys. Acta, 2009. 1789(4): p. 315-25 [PMID:18973837] Casson SA,Topping JF,Lindsey K MERISTEM-DEFECTIVE, an RS domain protein, is required for the correct meristem patterning and function in Arabidopsis. Plant J., 2009. 57(5): p. 857-69 [PMID:19000164] Miyashima S,Hashimoto T,Nakajima K ARGONAUTE1 acts in Arabidopsis root radial pattern formation independently of the SHR/SCR pathway. Plant Cell Physiol., 2009. 50(3): p. 626-34 [PMID:19188262] Cui H,Benfey PN Interplay between SCARECROW, GA and LIKE HETEROCHROMATIN PROTEIN 1 in ground tissue patterning in the Arabidopsis root. Plant J., 2009. 58(6): p. 1016-27 [PMID:19228333] Boggs NA,Dwyer KG,Nasrallah ME,Nasrallah JB In vivo detection of residues required for ligand-selective activation of the S-locus receptor in Arabidopsis. Curr. Biol., 2009. 19(9): p. 786-91 [PMID:19375322] Peer WA, et al. Mutation of the membrane-associated M1 protease APM1 results in distinct embryonic and seedling developmental defects in Arabidopsis. Plant Cell, 2009. 21(6): p. 1693-721 [PMID:19531600] Ticconi CA, et al. ER-resident proteins PDR2 and LPR1 mediate the developmental response of root meristems to phosphate availability. Proc. Natl. Acad. Sci. U.S.A., 2009. 106(33): p. 14174-9 [PMID:19666499] Carlsbecker A, et al. Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate. Nature, 2010. 465(7296): p. 316-21 [PMID:20410882] Pernas M,Ryan E,Dolan L SCHIZORIZA controls tissue system complexity in plants. Curr. Biol., 2010. 20(9): p. 818-23 [PMID:20417101] Ren G, et al. Reverse genetic identification of CRN1 and its distinctive role in chlorophyll degradation in Arabidopsis. J Integr Plant Biol, 2010. 52(5): p. 496-504 [PMID:20537045] Sozzani R, et al. Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth. Nature, 2010. 466(7302): p. 128-32 [PMID:20596025] Wang L,Mai YX,Zhang YC,Luo Q,Yang HQ MicroRNA171c-targeted SCL6-II, SCL6-III, and SCL6-IV genes regulate shoot branching in Arabidopsis. Mol Plant, 2010. 3(5): p. 794-806 [PMID:20720155] Dhondt S, et al. SHORT-ROOT and SCARECROW regulate leaf growth in Arabidopsis by stimulating S-phase progression of the cell cycle. Plant Physiol., 2010. 154(3): p. 1183-95 [PMID:20739610] Azpeitia E,Ben Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche. BMC Syst Biol, 2010. 4: p. 134 [PMID:20920363] Zhou W, et al. Arabidopsis Tyrosylprotein sulfotransferase acts in the auxin/PLETHORA pathway in regulating postembryonic maintenance of the root stem cell niche. Plant Cell, 2010. 22(11): p. 3692-709 [PMID:21045165] Kim K, et al. Phytochromes inhibit hypocotyl negative gravitropism by regulating the development of endodermal amyloplasts through phytochrome-interacting factors. Proc. Natl. Acad. Sci. U.S.A., 2011. 108(4): p. 1729-34 [PMID:21220341] Heo JO, et al. Funneling of gibberellin signaling by the GRAS transcription regulator scarecrow-like 3 in the Arabidopsis root. Proc. Natl. Acad. Sci. U.S.A., 2011. 108(5): p. 2166-71 [PMID:21245304] Sun X, et al. A functionally required unfoldome from the plant kingdom: intrinsically disordered N-terminal domains of GRAS proteins are involved in molecular recognition during plant development. Plant Mol. Biol., 2011. 77(3): p. 205-23 [PMID:21732203] Hern Apical meristem exhaustion during determinate primary root growth in the moots koom 1 mutant of Arabidopsis thaliana. Planta, 2011. 234(6): p. 1163-77 [PMID:21744091] Arabidopsis Interactome Mapping Consortium Evidence for network evolution in an Arabidopsis interactome map. Science, 2011. 333(6042): p. 601-7 [PMID:21798944] Koizumi K,Wu S,MacRae-Crerar A,Gallagher KL An essential protein that interacts with endosomes and promotes movement of the SHORT-ROOT transcription factor. Curr. Biol., 2011. 21(18): p. 1559-64 [PMID:21924907] Ogasawara H,Kaimi R,Colasanti J,Kozaki A Activity of transcription factor JACKDAW is essential for SHR/SCR-dependent activation of SCARECROW and MAGPIE and is modulated by reciprocal interactions with MAGPIE, SCARECROW and SHORT ROOT. Plant Mol. Biol., 2011. 77(4-5): p. 489-99 [PMID:21935722] Iyer-Pascuzzi AS, et al. Cell identity regulators link development and stress responses in the Arabidopsis root. Dev. Cell, 2011. 21(4): p. 770-82 [PMID:22014526] Cui H,Hao Y,Kong D SCARECROW has a SHORT-ROOT-independent role in modulating the sugar response. Plant Physiol., 2012. 158(4): p. 1769-78 [PMID:22312006] Pauluzzi G, et al. Surfing along the root ground tissue gene network. Dev. Biol., 2012. 365(1): p. 14-22 [PMID:22349629] Cui H Killing two birds with one stone: transcriptional regulators coordinate development and stress responses in plants. Plant Signal Behav, 2012. 7(6): p. 701-3 [PMID:22580500] Cruz-Ram A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division. Cell, 2012. 150(5): p. 1002-15 [PMID:22921914] Koizumi K,Hayashi T,Gallagher KL SCARECROW reinforces SHORT-ROOT signaling and inhibits periclinal cell divisions in the ground tissue by maintaining SHR at high levels in the endodermis. Plant Signal Behav, 2012. 7(12): p. 1573-7 [PMID:23072993] Koren D, et al. Strigolactone signaling in the endodermis is sufficient to restore root responses and involves SHORT HYPOCOTYL 2 (SHY2) activity. New Phytol., 2013. 198(3): p. 866-74 [PMID:23425316] Koizumi K,Gallagher KL Identification of SHRUBBY, a SHORT-ROOT and SCARECROW interacting protein that controls root growth and radial patterning. Development, 2013. 140(6): p. 1292-300 [PMID:23444357] Moubayidin L, et al. Spatial coordination between stem cell activity and cell differentiation in the root meristem. Dev. Cell, 2013. 26(4): p. 405-15 [PMID:23987513] Delmas F, et al. ABI3 controls embryo degreening through Mendel's I locus. Proc. Natl. Acad. Sci. U.S.A., 2013. 110(40): p. E3888-94 [PMID:24043799] Cruz-Ram A SCARECROW-RETINOBLASTOMA protein network controls protective quiescence in the Arabidopsis root stem cell organizer. PLoS Biol., 2013. 11(11): p. e1001724 [PMID:24302889] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Tian H,Jia Y,Niu T,Yu Q,Ding Z The key players of the primary root growth and development also function in lateral roots in Arabidopsis. Plant Cell Rep., 2014. 33(5): p. 745-53 [PMID:24504658] Cui H,Kong D,Liu X,Hao Y SCARECROW, SCR-LIKE 23 and SHORT-ROOT control bundle sheath cell fate and function in Arabidopsis thaliana. Plant J., 2014. 78(2): p. 319-27 [PMID:24517883] Reyes-Hernández BJ, et al. The root indeterminacy-to-determinacy developmental switch is operated through a folate-dependent pathway in Arabidopsis thaliana. New Phytol., 2014. 202(4): p. 1223-36 [PMID:24635769] Wang Z,Mao JL,Zhao YJ,Li CY,Xiang CB L-Cysteine inhibits root elongation through auxin/PLETHORA and SCR/SHR pathway in Arabidopsis thaliana. J Integr Plant Biol, 2015. 57(2): p. 186-97 [PMID:24798139] Gao X,Wang C,Cui H Identification of bundle sheath cell fate factors provides new tools for C3-to-C4 engineering. Plant Signal Behav, 2018. [PMID:24819776] Ron M, et al. Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model. Plant Physiol., 2014. 166(2): p. 455-69 [PMID:24868032] Wu S, et al. A plausible mechanism, based upon Short-Root movement, for regulating the number of cortex cell layers in roots. Proc. Natl. Acad. Sci. U.S.A., 2014. 111(45): p. 16184-9 [PMID:25352666] Della Rovere F, et al. Arabidopsis SHR and SCR transcription factors and AUX1 auxin influx carrier control the switch between adventitious rooting and xylogenesis in planta and in in Ann. Bot., 2015. 115(4): p. 617-28 [PMID:25617411] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] Jia Y, et al. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. J. Exp. Bot., 2015. 66(15): p. 4631-42 [PMID:25998905] Zhang M, et al. A tetratricopeptide repeat domain-containing protein SSR1 located in mitochondria is involved in root development and auxin polar transport in Arabidopsis. Plant J., 2015. 83(4): p. 582-99 [PMID:26072661] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755] Gong X, et al. SEUSS Integrates Gibberellin Signaling with Transcriptional Inputs from the SHR-SCR-SCL3 Module to Regulate Middle Cortex Formation in the Arabidopsis Root. Plant Physiol., 2016. 170(3): p. 1675-83 [PMID:26818732] Moubayidin L, et al. A SCARECROW-based regulatory circuit controls Arabidopsis thaliana meristem size from the root endodermis. Planta, 2016. 243(5): p. 1159-68 [PMID:26848984] Madmon O, et al. Expression of MAX2 under SCARECROW promoter enhances the strigolactone/MAX2 dependent response of Arabidopsis roots to low-phosphate conditions. Planta, 2016. 243(6): p. 1419-27 [PMID:26919985] Lee SA, et al. Interplay between ABA and GA Modulates the Timing of Asymmetric Cell Divisions in the Arabidopsis Root Ground Tissue. Mol Plant, 2016. 9(6): p. 870-84 [PMID:26970019] Benfey PN Defining the Path from Stem Cells to Differentiated Tissue. Curr. Top. Dev. Biol., 2016. 116: p. 35-43 [PMID:26970612] Li Q,Zhao Y,Yue M,Xue Y,Bao S The Protein Arginine Methylase 5 (PRMT5/SKB1) Gene Is Required for the Maintenance of Root Stem Cells in Response to DNA Damage. J Genet Genomics, 2016. 43(4): p. 187-97 [PMID:27090604] Clark NM, et al. Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy. Elife, 2017. [PMID:27288545] Choi JW,Lim J Control of Asymmetric Cell Divisions during Root Ground Tissue Maturation. Mol. Cells, 2016. 39(7): p. 524-9 [PMID:27306644] Yoon EK, et al. Conservation and Diversification of the SHR-SCR-SCL23 Regulatory Network in the Development of the Functional Endodermis in Arabidopsis Shoots. Mol Plant, 2016. 9(8): p. 1197-1209 [PMID:27353361] Waszczak C, et al. SHORT-ROOT Deficiency Alleviates the Cell Death Phenotype of the Arabidopsis catalase2 Mutant under Photorespiration-Promoting Conditions. Plant Cell, 2016. 28(8): p. 1844-59 [PMID:27432873] Goh T, et al. Quiescent center initiation in the Arabidopsis lateral root primordia is dependent on the SCARECROW transcription factor. Development, 2016. 143(18): p. 3363-71 [PMID:27510971] Yu Q, et al. A P-Loop NTPase Regulates Quiescent Center Cell Division and Distal Stem Cell Identity through the Regulation of ROS Homeostasis in Arabidopsis Root. PLoS Genet., 2016. 12(9): p. e1006175 [PMID:27583367] Sparks EE, et al. Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors. Dev. Cell, 2016. 39(5): p. 585-596 [PMID:27923776] Hirano Y, et al. Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD. Nat Plants, 2017. 3: p. 17010 [PMID:28211915] Kobayashi A,Miura S,Kozaki A INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves. Plant Mol. Biol., 2017. 94(1-2): p. 1-13 [PMID:28324206] Díaz-Triviño S,Long Y,Scheres B,Blilou I Analysis of a Plant Transcriptional Regulatory Network Using Transient Expression Systems. Methods Mol. Biol., 2017. 1629: p. 83-103 [PMID:28623581] Long Y, et al. In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots. Nature, 2017. 548(7665): p. 97-102 [PMID:28746306] Bruno L, et al. In Arabidopsis thaliana Cadmium Impact on the Growth of Primary Root by Altering SCR Expression and Auxin-Cytokinin Cross-Talk. Front Plant Sci, 2017. 8: p. 1323 [PMID:28798767] Mira MM, et al. Expression of Arabidopsis class 1 phytoglobin (AtPgb1) delays death and degradation of the root apical meristem during severe PEG-induced water deficit. J. Exp. Bot., 2017. 68(20): p. 5653-5668 [PMID:29059380] Bustillo-Avendaño E, et al. Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis. Plant Physiol., 2018. 176(2): p. 1709-1727 [PMID:29233938] Ercoli MF, et al. GIF Transcriptional Coregulators Control Root Meristem Homeostasis. Plant Cell, 2018. 30(2): p. 347-359 [PMID:29352064] Shimotohno A,Heidstra R,Blilou I,Scheres B Root stem cell niche organizer specification by molecular convergence of PLETHORA and SCARECROW transcription factor modules. Genes Dev., 2018. 32(15-16): p. 1085-1100 [PMID:30018102] Di Laurenzio L, et al. The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root. Cell, 1996. 86(3): p. 423-33 [PMID:8756724] Fukaki H,Fujisawa H,Tasaka M SGR1, SGR2, SGR3: novel genetic loci involved in shoot gravitropism in Arabidopsis thaliana. Plant Physiol., 1996. 110(3): p. 945-55 [PMID:8819871] Yamauchi Y,Fukaki H,Fujisawa H,Tasaka M Mutations in the SGR4, SGR5 and SGR6 loci of Arabidopsis thaliana alter the shoot gravitropism. Plant Cell Physiol., 1997. 38(5): p. 530-5 [PMID:9210330] Truong HN,Caboche M,Daniel-Vedele F Sequence and characterization of two Arabidopsis thaliana cDNAs isolated by functional complementation of a yeast gln3 gdh1 mutant. FEBS Lett., 1997. 410(2-3): p. 213-8 [PMID:9237632] Malamy JE,Benfey PN Analysis of SCARECROW expression using a rapid system for assessing transgene expression in Arabidopsis roots. Plant J., 1997. 12(4): p. 957-63 [PMID:9375406] Wysocka-Diller JW,Benfey PN Root development: signaling down and around. Bioessays, 1997. 19(11): p. 959-65 [PMID:9394618] Silverstone AL,Ciampaglio CN,Sun T The Arabidopsis RGA gene encodes a transcriptional regulator repressing the gibberellin signal transduction pathway. Plant Cell, 1998. 10(2): p. 155-69 [PMID:9490740] Fukaki H, et al. Genetic evidence that the endodermis is essential for shoot gravitropism in Arabidopsis thaliana. Plant J., 1998. 14(4): p. 425-30 [PMID:9670559]