CLE41_ARATH
ID CLE41_ARATH Reviewed; 99 AA.
AC Q84W98; Q8LB23;
DT 30-NOV-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 93.
DE RecName: Full=CLAVATA3/ESR (CLE)-related protein 41 {ECO:0000303|PubMed:16489133};
DE AltName: Full=Tracheary element differentiation inhibitory factor-like protein {ECO:0000303|PubMed:16902140};
DE Short=TDIF-like protein {ECO:0000303|PubMed:16902140};
DE Contains:
DE RecName: Full=CLE41p {ECO:0000303|PubMed:16489133};
DE Flags: Precursor;
GN Name=CLE41 {ECO:0000303|PubMed:16489133};
GN OrderedLocusNames=At3g24770 {ECO:0000312|Araport:AT3G24770};
GN ORFNames=K7P8.35 {ECO:0000312|EMBL:AB028609};
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=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(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].
RC STRAIN=cv. Columbia;
RA Cheuk R.F., Chen H., Kim C.J., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (JAN-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
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 [6]
RP TISSUE SPECIFICITY, AND GENE FAMILY.
RX PubMed=16489133; DOI=10.1104/pp.105.075515;
RA Strabala T.J., O'donnell P.J., Smit A.-M., Ampomah-Dwamena C., Martin E.J.,
RA Netzler N., Nieuwenhuizen N.J., Quinn B.D., Foote H.C.C., Hudson K.R.;
RT "Gain-of-function phenotypes of many CLAVATA3/ESR genes, including four new
RT family members, correlate with tandem variations in the conserved
RT CLAVATA3/ESR domain.";
RL Plant Physiol. 140:1331-1344(2006).
RN [7]
RP FUNCTION.
RX PubMed=16902140; DOI=10.1126/science.1128436;
RA Ito Y., Nakanomyo I., Motose H., Iwamoto K., Sawa S., Dohmae N., Fukuda H.;
RT "Dodeca-CLE peptides as suppressors of plant stem cell differentiation.";
RL Science 313:842-845(2006).
RN [8]
RP REVIEW.
RX PubMed=18034320; DOI=10.1007/s00018-007-7411-5;
RA Jun J.H., Fiume E., Fletcher J.C.;
RT "The CLE family of plant polypeptide signaling molecules.";
RL Cell. Mol. Life Sci. 65:743-755(2008).
RN [9]
RP REVIEW.
RX PubMed=18078779; DOI=10.1016/j.pbi.2007.10.010;
RA Mitchum M.G., Wang X., Davis E.L.;
RT "Diverse and conserved roles of CLE peptides.";
RL Curr. Opin. Plant Biol. 11:75-81(2008).
RN [10]
RP FUNCTION, MUTAGENESIS OF PRO-94, INTERACTION WITH TDR, TISSUE SPECIFICITY,
RP AND SUBCELLULAR LOCATION.
RX PubMed=18812507; DOI=10.1073/pnas.0808444105;
RA Hirakawa Y., Shinohara H., Kondo Y., Inoue A., Nakanomyo I., Ogawa M.,
RA Sawa S., Ohashi-Ito K., Matsubayashi Y., Fukuda H.;
RT "Non-cell-autonomous control of vascular stem cell fate by a CLE
RT peptide/receptor system.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:15208-15213(2008).
RN [11]
RP FUNCTION.
RX PubMed=19011104; DOI=10.1073/pnas.0809395105;
RA Whitford R., Fernandez A., De Groodt R., Ortega E., Hilson P.;
RT "Plant CLE peptides from two distinct functional classes synergistically
RT induce division of vascular cells.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:18625-18630(2008).
RN [12]
RP REVIEW.
RX PubMed=20016993; DOI=10.1007/s00709-009-0095-y;
RA Wang G., Fiers M.;
RT "CLE peptide signaling during plant development.";
RL Protoplasma 240:33-43(2010).
RN [13]
RP FUNCTION.
RC STRAIN=cv. Columbia;
RX PubMed=28607033; DOI=10.15252/embr.201643535;
RA Hazak O., Brandt B., Cattaneo P., Santiago J., Rodriguez-Villalon A.,
RA Hothorn M., Hardtke C.S.;
RT "Perception of root-active CLE peptides requires CORYNE function in the
RT phloem vasculature.";
RL EMBO Rep. 18:1367-1381(2017).
RN [14]
RP STRUCTURE BY NMR OF 88-99.
RA DiGennaro P.M., Bobay B.G., Bird D.M.;
RT "Inferring function of CLE peptides from high resolution tertiary
RT structures.";
RL Submitted (DEC-2013) to the PDB data bank.
RN [15]
RP X-RAY CRYSTALLOGRAPHY (2.77 ANGSTROMS) OF 88-99 IN COMPLEX WITH TDR, AND
RP MUTAGENESIS OF HIS-88; VAL-90; GLY-93; ASN-95; PRO-96; SER-98 AND ASN-99.
RX PubMed=27055373; DOI=10.1038/cr.2016.45;
RA Zhang H., Lin X., Han Z., Qu L.-J., Chai J.;
RT "Crystal structure of PXY-TDIF complex reveals a conserved recognition
RT mechanism among CLE peptide-receptor pairs.";
RL Cell Res. 26:543-555(2016).
RN [16]
RP X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) OF 88-99 IN COMPLEX WITH TDR.
RX PubMed=27498761; DOI=10.1038/ncomms12383;
RA Morita J., Kato K., Nakane T., Kondo Y., Fukuda H., Nishimasu H.,
RA Ishitani R., Nureki O.;
RT "Crystal structure of the plant receptor-like kinase TDR in complex with
RT the TDIF peptide.";
RL Nat. Commun. 7:12383-12383(2016).
RN [17]
RP X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) OF 88-99.
RA Xu G., Li Z.;
RT "Crystal structure of a TDIF-TDR complex.";
RL Submitted (APR-2016) to the PDB data bank.
CC -!- FUNCTION: [CLE41p]: Extracellular signal peptide that regulates cell
CC fate. May act with TDR as a ligand-receptor pair in a signal
CC transduction pathway that represses tracheary element differentiation
CC but promotes the formation of procambial cells adjacent to phloem cells
CC in the veins in an auxin-dependent manner. Regulates the transition of
CC protophloem cells from proliferation to differentiation, thus impinging
CC on postembryonic growth capacity of the root meristem; this signaling
CC pathway requires CRN and CLV2 (PubMed:28607033).
CC {ECO:0000269|PubMed:16902140, ECO:0000269|PubMed:18812507,
CC ECO:0000269|PubMed:19011104, ECO:0000269|PubMed:28607033}.
CC -!- SUBUNIT: [CLE41p]: CLE41p interacts specifically with the leucine-rich
CC repeat receptor-like protein kinase TDR. {ECO:0000269|PubMed:18812507,
CC ECO:0000269|PubMed:27055373, ECO:0000269|PubMed:27498761}.
CC -!- SUBCELLULAR LOCATION: [CLE41p]: Secreted, extracellular space
CC {ECO:0000269|PubMed:18812507}. Note=Probably secreted from the phloem
CC cells and distributed in the procambial region.
CC {ECO:0000269|PubMed:18812507}.
CC -!- TISSUE SPECIFICITY: [CLE41p]: Mostly expressed in inflorescence and
CC roots, and, to a lower extent, in seedlings, flowers, leaves and
CC siliques. Observed along the vascular strands in cotyledons, leaves and
CC roots, but not in shoot apical meristems (SAM). Restricted to the
CC phloem and the neighboring pericycle cells in the roots and hypocotyls.
CC {ECO:0000269|PubMed:16489133, ECO:0000269|PubMed:18812507}.
CC -!- PTM: [CLE41p]: The O-glycosylation (arabinosylation) of the
CC hydroxyproline Pro-94 enhances binding affinity of the CLE41p peptide
CC for its receptor. {ECO:0000250|UniProtKB:O49519}.
CC -!- SIMILARITY: Belongs to the CLV3/ESR signal peptide family.
CC {ECO:0000305}.
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DR EMBL; AB028609; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002686; AEE76945.1; -; Genomic_DNA.
DR EMBL; BT004087; AAO42114.1; -; mRNA.
DR EMBL; BT020560; AAW70406.1; -; mRNA.
DR EMBL; AY087469; AAM67331.1; -; mRNA.
DR RefSeq; NP_566754.1; NM_113389.1.
DR PDB; 5GIJ; X-ray; 3.00 A; D=88-99.
DR PDB; 5GR9; X-ray; 2.77 A; C=88-99.
DR PDB; 5JFI; X-ray; 2.75 A; C/D=88-99.
DR PDBsum; 5GIJ; -.
DR PDBsum; 5GR9; -.
DR PDBsum; 5JFI; -.
DR AlphaFoldDB; Q84W98; -.
DR SMR; Q84W98; -.
DR STRING; 3702.AT3G24770.1; -.
DR PaxDb; Q84W98; -.
DR PRIDE; Q84W98; -.
DR EnsemblPlants; AT3G24770.1; AT3G24770.1; AT3G24770.
DR GeneID; 822075; -.
DR Gramene; AT3G24770.1; AT3G24770.1; AT3G24770.
DR KEGG; ath:AT3G24770; -.
DR Araport; AT3G24770; -.
DR TAIR; locus:2087328; AT3G24770.
DR HOGENOM; CLU_161000_0_0_1; -.
DR InParanoid; Q84W98; -.
DR OMA; MTHHRST; -.
DR OrthoDB; 1527064at2759; -.
DR PhylomeDB; Q84W98; -.
DR PRO; PR:Q84W98; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q84W98; baseline and differential.
DR Genevisible; Q84W98; AT.
DR GO; GO:0048046; C:apoplast; IDA:UniProtKB.
DR GO; GO:0005615; C:extracellular space; IEA:UniProtKB-SubCell.
DR GO; GO:0033612; F:receptor serine/threonine kinase binding; IPI:UniProtKB.
DR GO; GO:0090506; P:axillary shoot meristem initiation; IDA:TAIR.
DR GO; GO:0051301; P:cell division; IMP:TAIR.
DR GO; GO:0045168; P:cell-cell signaling involved in cell fate commitment; ISS:UniProtKB.
DR GO; GO:0010078; P:maintenance of root meristem identity; IDA:UniProtKB.
DR GO; GO:0010088; P:phloem development; IDA:UniProtKB.
DR GO; GO:0010087; P:phloem or xylem histogenesis; IDA:TAIR.
DR GO; GO:0010067; P:procambium histogenesis; IDA:UniProtKB.
DR GO; GO:0045595; P:regulation of cell differentiation; IDA:UniProtKB.
DR GO; GO:0010223; P:secondary shoot formation; IMP:TAIR.
DR GO; GO:0010089; P:xylem development; IDA:UniProtKB.
DR InterPro; IPR037495; CLE41/42/44.
DR PANTHER; PTHR35301; PTHR35301; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Developmental protein; Differentiation; Glycoprotein;
KW Hydroxylation; Reference proteome; Secreted; Signal.
FT SIGNAL 1..34
FT /evidence="ECO:0000255"
FT CHAIN 35..99
FT /note="CLAVATA3/ESR (CLE)-related protein 41"
FT /id="PRO_0000401283"
FT PEPTIDE 88..99
FT /note="CLE41p"
FT /evidence="ECO:0000250|UniProtKB:O49519"
FT /id="PRO_0000401284"
FT REGION 60..99
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 69..87
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 91
FT /note="Hydroxyproline"
FT /evidence="ECO:0000250|UniProtKB:O49519"
FT MOD_RES 94
FT /note="Hydroxyproline"
FT /evidence="ECO:0000250|UniProtKB:O49519"
FT CARBOHYD 94
FT /note="O-linked (Ara...) hydroxyproline"
FT /evidence="ECO:0000250|UniProtKB:O49519"
FT MUTAGEN 88
FT /note="H->R: Compromised interaction with TDR."
FT /evidence="ECO:0000269|PubMed:27055373"
FT MUTAGEN 90
FT /note="V->H: Compromised interaction with TDR."
FT /evidence="ECO:0000269|PubMed:27055373"
FT MUTAGEN 93
FT /note="G->A: Compromised interaction with TDR."
FT /evidence="ECO:0000269|PubMed:27055373"
FT MUTAGEN 94
FT /note="P->A: Impaired repression of tracheary element
FT differentiation."
FT /evidence="ECO:0000269|PubMed:18812507"
FT MUTAGEN 95
FT /note="N->L: Compromised interaction with TDR."
FT /evidence="ECO:0000269|PubMed:27055373"
FT MUTAGEN 96
FT /note="P->A: Compromised interaction with TDR."
FT /evidence="ECO:0000269|PubMed:27055373"
FT MUTAGEN 98
FT /note="S->H: Compromised interaction with TDR."
FT /evidence="ECO:0000269|PubMed:27055373"
FT MUTAGEN 99
FT /note="N->A: Compromised interaction with TDR."
FT /evidence="ECO:0000269|PubMed:27055373"
FT MUTAGEN 99
FT /note="N->NR: Compromised interaction with TDR."
FT /evidence="ECO:0000269|PubMed:27055373"
FT CONFLICT 16..22
FT /note="RTLLLLF -> HTRLLLL (in Ref. 5; AAM67331)"
FT /evidence="ECO:0000305"
FT CONFLICT 74
FT /note="R -> P (in Ref. 5; AAM67331)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 99 AA; 11018 MW; 5783BB10E723C656 CRC64;
MATSNDQTNT KSSHSRTLLL LFIFLSLLLF SSLTIPMTRH QSTSMVAPFK RVLLESSVPA
SSTMDLRPKA STRRSRTSRR REFGNDAHEV PSGPNPISN
