CLE40_ARATH
ID CLE40_ARATH Reviewed; 80 AA.
AC Q9LXU0;
DT 30-NOV-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 83.
DE RecName: Full=CLAVATA3/ESR (CLE)-related protein 40 {ECO:0000303|PubMed:16489133};
DE Contains:
DE RecName: Full=CLE40p {ECO:0000303|PubMed:16489133};
DE Flags: Precursor;
GN Name=CLE40 {ECO:0000303|PubMed:16489133};
GN OrderedLocusNames=At5g12990 {ECO:0000312|Araport:AT5G12990};
GN ORFNames=T24H18.160 {ECO:0000312|EMBL:CAB88263.1};
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], AND SUBCELLULAR LOCATION.
RX PubMed=12602871; DOI=10.1023/a:1022038932376;
RA Sharma V.K., Ramirez J., Fletcher J.C.;
RT "The Arabidopsis CLV3-like (CLE) genes are expressed in diverse tissues and
RT encode secreted proteins.";
RL Plant Mol. Biol. 51:415-425(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
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 GENE FAMILY, AND NOMENCLATURE.
RX PubMed=11457943; DOI=10.1104/pp.126.3.939;
RA Cock J.M., McCormick S.;
RT "A large family of genes that share homology with CLAVATA3.";
RL Plant Physiol. 126:939-942(2001).
RN [5]
RP FUNCTION, TISSUE SPECIFICITY, AND DISRUPTION PHENOTYPE.
RX PubMed=12743822; DOI=10.1007/s00427-003-0329-5;
RA Hobe M., Mueller R., Gruenewald M., Brand U., Simon R.;
RT "Loss of CLE40, a protein functionally equivalent to the stem cell
RT restricting signal CLV3, enhances root waving in Arabidopsis.";
RL Dev. Genes Evol. 213:371-381(2003).
RN [6]
RP FUNCTION.
RX PubMed=16055633; DOI=10.1105/tpc.105.034009;
RA Fiers M., Golemiec E., Xu J., van der Geest L., Heidstra R., Stiekema W.,
RA Liu C.-M.;
RT "The 14-amino acid CLV3, CLE19, and CLE40 peptides trigger consumption of
RT the root meristem in Arabidopsis through a CLAVATA2-dependent pathway.";
RL Plant Cell 17:2542-2553(2005).
RN [7]
RP 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 [8]
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 [9]
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 [10]
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 [11]
RP FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=19398337; DOI=10.1016/j.cub.2009.03.060;
RA Stahl Y., Wink R.H., Ingram G.C., Simon R.;
RT "A signaling module controlling the stem cell niche in Arabidopsis root
RT meristems.";
RL Curr. Biol. 19:909-914(2009).
RN [12]
RP FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=19820344; DOI=10.4161/psb.4.7.8970;
RA Stahl Y., Simon R.;
RT "Is the Arabidopsis root niche protected by sequestration of the CLE40
RT signal by its putative receptor ACR4.";
RL Plant Signal. Behav. 4:634-635(2009).
RN [13]
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 [14]
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).
CC -!- FUNCTION: [CLE40p]: Extracellular signal peptide secreted by
CC differentiated root cells that regulates root cell fate. Acts with ACR4
CC as a ligand-receptor pair in a signal transduction pathway,
CC coordinating movement of the root tip and organization of cell
CC divisions in the root meristem. Promotes cell differentiation in the
CC distal root meristem in a dose-dependent manner, especially the
CC transition from columella stem cells (CSC) daughters into columella
CC cells (CCs). Induces ACR4 expression in root quiescent center (QC).
CC Involved in WUX5 QC-specific expression pattern regulation. Regulates
CC the transition of protophloem cells from proliferation to
CC differentiation, thus impinging on postembryonic growth capacity of the
CC root meristem; this signaling pathway requires CRN and CLV2
CC (PubMed:28607033). {ECO:0000269|PubMed:12743822,
CC ECO:0000269|PubMed:16055633, ECO:0000269|PubMed:16902140,
CC ECO:0000269|PubMed:19398337, ECO:0000269|PubMed:19820344,
CC ECO:0000269|PubMed:28607033}.
CC -!- SUBCELLULAR LOCATION: [CLE40p]: Secreted, extracellular space
CC {ECO:0000269|PubMed:12602871}.
CC -!- TISSUE SPECIFICITY: [CLE40p]: Mostly expressed at low levels in stems
CC and apex, and, to a lower extent, in roots, seedlings, leaves, flowers,
CC siliques and pollen. {ECO:0000269|PubMed:12743822,
CC ECO:0000269|PubMed:19398337, ECO:0000269|PubMed:19820344}.
CC -!- DEVELOPMENTAL STAGE: [CLE40p]: Expressed in the entire embryo at the
CC globular stage. Progressively restricted to the basal regions of the
CC embryo that form the root meristem and the vasculature. After
CC germination, detected in the differentiation zone of the stele that
CC forms the inner layers of the root and in differentiating columella
CC cells (CCs). {ECO:0000269|PubMed:19398337,
CC ECO:0000269|PubMed:19820344}.
CC -!- DISRUPTION PHENOTYPE: [CLE40p]: Short roots with irregularly shaped
CC root tips and following a waving pattern. Delayed differentiation of
CC columella stem cells (CSC) daughters into columella cells (CCs).
CC {ECO:0000269|PubMed:12743822, ECO:0000269|PubMed:19398337,
CC ECO:0000269|PubMed:19820344}.
CC -!- SIMILARITY: Belongs to the CLV3/ESR signal peptide family.
CC {ECO:0000305}.
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DR EMBL; AL353013; CAB88263.1; -; Genomic_DNA.
DR EMBL; CP002688; AED91838.1; -; Genomic_DNA.
DR PIR; T49913; T49913.
DR RefSeq; NP_196803.1; NM_121302.2.
DR AlphaFoldDB; Q9LXU0; -.
DR SMR; Q9LXU0; -.
DR STRING; 3702.AT5G12990.1; -.
DR PaxDb; Q9LXU0; -.
DR PRIDE; Q9LXU0; -.
DR EnsemblPlants; AT5G12990.1; AT5G12990.1; AT5G12990.
DR GeneID; 831139; -.
DR Gramene; AT5G12990.1; AT5G12990.1; AT5G12990.
DR KEGG; ath:AT5G12990; -.
DR Araport; AT5G12990; -.
DR TAIR; locus:2182325; AT5G12990.
DR HOGENOM; CLU_2530591_0_0_1; -.
DR InParanoid; Q9LXU0; -.
DR OMA; FWLGETQ; -.
DR OrthoDB; 1588010at2759; -.
DR PRO; PR:Q9LXU0; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9LXU0; baseline and differential.
DR Genevisible; Q9LXU0; AT.
DR GO; GO:0048046; C:apoplast; ISM:TAIR.
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:0001708; P:cell fate specification; 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:0045595; P:regulation of cell differentiation; IDA:UniProtKB.
PE 2: Evidence at transcript level;
KW Developmental protein; Differentiation; Hydroxylation; Reference proteome;
KW Secreted; Signal.
FT SIGNAL 1..25
FT /evidence="ECO:0000255"
FT CHAIN 26..80
FT /note="CLAVATA3/ESR (CLE)-related protein 40"
FT /id="PRO_0000401281"
FT PEPTIDE 62..73
FT /note="CLE40p"
FT /evidence="ECO:0000250|UniProtKB:O49519"
FT /id="PRO_0000401282"
FT REGION 45..80
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 65
FT /note="Hydroxyproline"
FT /evidence="ECO:0000250|UniProtKB:O49519"
SQ SEQUENCE 80 AA; 8856 MW; 907BC07E42C7EA09 CRC64;
MAAMKYKGSV FIILVILLLS SSLLAHSSST KSFFWLGETQ DTKAMKKEKK IDGGTANEVE
ERQVPTGSDP LHHKHIPFTP
