# Research Progress of CLE and Its Prospects in Woody Plants

**Authors:** Zewen Song, Wenjun Zhou, Hanyu Jiang, Yifan Duan

PMC · DOI: 10.3390/plants14101424 · Plants · 2025-05-09

## TL;DR

This review summarizes the role of CLE peptides in plant development, focusing on their signaling functions in various meristems and their potential in woody plants.

## Contribution

The paper provides a comprehensive overview of CLE gene functions in different plant meristems and highlights their evolutionary conservation.

## Key findings

- CLE genes regulate multiple meristems, including root and shoot apical meristems.
- CLE peptides are involved in various signaling pathways and developmental processes.
- The study emphasizes the need for further research on CLE functions in tall trees.

## Abstract

The peptide ligands of the CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) family have been previously identified as essential signals for both short- and long-distance communication in plants, particularly during stem cell homeostasis, cell fate determination, and growth and development. To date, most studies on the CLE family have focused on model plants and especially those involving stem and apical meristems. Relatively little is known about the role of CLE peptides in tall trees and other plant meristems. In this review, we summarize the role of CLE genes in regulating plant Root Apical Meristem (RAM), Shoot Apical Meristem (SAM), Procambium, Leaf and Floral Meristem (FM), as well as their involvement in multiple signaling pathways. We also highlight the evolutionary conservation of the CLE gene family and provide a comprehensive summary of its distribution across various plant developmental tissues. This paper aims to provide insights into novel regulatory networks of CLE in plant meristems, offering guidance for understanding intercellular signaling pathways in forest trees and the development of new plant organs.

## Linked entities

- **Genes:** EIF2B5 (eukaryotic translation initiation factor 2B subunit epsilon) [NCBI Gene 8893]

## Full-text entities

- **Genes:** CLE27 (CLAVATA3/ESR-RELATED 27) [NCBI Gene 822187] {aka CLAVATA3/ESR-RELATED 27}, SlCLE9 [NCBI Gene 115600545], RPK2 (receptor-like protein kinase 2) [NCBI Gene 821240] {aka CLI1, F1C9.8, F1C9_8, TOAD2, TOADSTOOL 2, clv3 peptide insensitive 1}, ESR1 [NCBI Gene 100037781], CLV2 (Leucine-rich repeat (LRR) family protein) [NCBI Gene 842849] {aka AtRLP10, Receptor Like Protein 10, T8F5.16, T8F5_16, clavata 2}, FKF1 (flavin-binding, kelch repeat, f box 1) [NCBI Gene 843133] {aka ''flavin-binding, ADO3, T23K23.10, T23K23_10, f box 1, f box 1''}, CLE45 (CLAVATA3/ESR-RELATED 45) [NCBI Gene 5007842] {aka CLAVATA3/ESR-RELATED 45}, APX1 (ascorbate peroxidase 1) [NCBI Gene 837304] {aka ASCORBATE PEROXIDASE, ATAPX01, ATAPX1, CS1, F24B9.2, F24B9_2}, APX3 (ascorbate peroxidase 3) [NCBI Gene 829652] {aka ASCORBATE PEROXIDASE 3, M4E13.60, M4E13_60, ascorbate peroxidase 3}, CLE16 (CLAVATA3/ESR-RELATED 16) [NCBI Gene 28717514] {aka CLAVATA3/ESR-RELATED 16}, BRX (DZC (Disease resistance/zinc finger/chromosome condensation-like region) domain containing protein) [NCBI Gene 840078] {aka BREVIS RADIX, F5M6.11, F5M6_11, NIP3;1, NLM9, NOD26-like intrinsic protein 3;1}, ESR1 (Integrase-type DNA-binding superfamily protein) [NCBI Gene 837856] {aka DORNROSCHEN, DRN, ENHANCER OF SHOOT REGENERATION 1, F3F19.1, F3F19_1}, WOX1 (WUSCHEL related homeobox 1) [NCBI Gene 821325] {aka WUSCHEL related homeobox 1}, CLE1 (CLAVATA3/ESR-RELATED 1) [NCBI Gene 28717420] {aka CLAVATA3/ESR-RELATED 1}, CLE25 (CLAVATA3/ESR-RELATED 25) [NCBI Gene 822475] {aka CLAVATA3/ESR-RELATED 25}, WOX5 (WUSCHEL related homeobox 5) [NCBI Gene 820297] {aka WOX5B, WUSCHEL related homeobox 5, WUSCHEL related homeobox 5B}, HAE (Leucine-rich receptor-like protein kinase family protein) [NCBI Gene 828967] {aka F20O9.180, F20O9_180, HAESA, RECEPTOR-LIKE PROTEIN KINASE 5, RLK5}, BAM3 (Leucine-rich receptor-like protein kinase family protein) [NCBI Gene 827774] {aka BARELY ANY MERISTEM 3, F1C12.190, F1C12_190}, MAKR5 (membrane-associated kinase regulator) [NCBI Gene 835364] {aka MEMBRANE-ASSOCIATED KINASE REGULATOR 5, MXC20.9, MXC20_9}, CLE11 (CLAVATA3/ESR-RELATED 11) [NCBI Gene 841323] {aka CLAVATA3/ESR-RELATED 11}, EIN3 (Ethylene insensitive 3 family protein) [NCBI Gene 821625] {aka AtEIN3, ETHYLENE-INSENSITIVE3}, SPCH (basic helix-loop-helix (bHLH) DNA-binding superfamily protein) [NCBI Gene 835402] {aka MFH8.15, SPEECHLESS}, CLE26 (CLAVATA3/ESR-RELATED 26) [NCBI Gene 843334] {aka CLAVATA3/ESR-RELATED 26, F20P5.29, F20P5_29}, PIN1 (Auxin efflux carrier family protein) [NCBI Gene 843693] {aka ARABIDOPSIS THALIANA PIN-FORMED 1, ATPIN1, F6D5.2, F6D5_2, PIN-FORMED 1}, STM (KNOX/ELK homeobox transcription factor) [NCBI Gene 842534] {aka BUM, BUM1, BUMBERSHOOT, BUMBERSHOOT 1, F24O1.38, F24O1_38}, CLE4 (CLAVATA3/ESR-RELATED 4) [NCBI Gene 817661] {aka CLAVATA3/ESR-RELATED 4}, NDL1 (N-MYC downregulated-like 1) [NCBI Gene 835777] {aka MIK19.22, MIK19_22, N-MYC downregulated-like 1}, PXY (Leucine-rich repeat protein kinase family protein) [NCBI Gene 836269] {aka MCI2.4, MCI2_4, PHLOEM INTERCALATED WITH XYLEM, TDIF receptor, TDR}, CLV3 (CLAVATA3) [NCBI Gene 817267] {aka AtCLV3, CLAVATA3, F12K2.17, F12K2_17}, MPK6 (MAP kinase 6) [NCBI Gene 818982] {aka ATMAPK6, ATMPK6, F18O19.10, MAP KINASE 6, MAP kinase 6, MAPK6}, CLE14 (CLAVATA3/ESR-RELATED 14) [NCBI Gene 28717391] {aka CLAVATA3/ESR-RELATED 14}, CLE21 (CLAVATA3/ESR-RELATED 21) [NCBI Gene 28721288] {aka CLAVATA3/ESR-RELATED 21, MXK3.2, MXK3_2}, BOP1 (Ankyrin repeat family protein / BTB/POZ domain-containing protein) [NCBI Gene 824880] {aka BLADE ON PETIOLE 1}, POL (Protein phosphatase 2C family protein) [NCBI Gene 819306] {aka F14M4.25, poltergeist}, CLE6 (CLAVATA3/ESR-RELATED 6) [NCBI Gene 817664] {aka AtCLE6, CLAVATA3/ESR-RELATED 6}, CLE3 (CLAVATA3/ESR-RELATED 3) [NCBI Gene 837132] {aka CLAVATA3/ESR-RELATED 3}, CLE5 (CLAVATA3/ESR-RELATED 5) [NCBI Gene 817663] {aka AtCLE5, CLAVATA3/ESR-RELATED 5}, BRM (transcription regulatory protein SNF2) [NCBI Gene 819210] {aka ARABIDOPSIS THALIANA BRAHMA, ATBRM, BRAHMA, CHA2, CHR2, CHROMATIN REMODELING 2}, CLE17 (CLAVATA3/ESR-RELATED 17) [NCBI Gene 843428] {aka CLAVATA3/ESR-RELATED 17}, CAT3 (catalase 3) [NCBI Gene 838651] {aka ATCAT3, F5M15.5, F5M15_5, SEN2, SENESCENCE 2, catalase 3}, MPK3 (mitogen-activated protein kinase 3) [NCBI Gene 823706] {aka ATMAPK3, ATMPK3, T6D9.4, mitogen-activated protein kinase 3}, PLL1 (poltergeist like 1) [NCBI Gene 818102] {aka T32F12.27, T32F12_27, poltergeist like 1}, CLE10 (CLAVATA3/ESR-RELATED 10) [NCBI Gene 843263] {aka CLAVATA3/ESR-RELATED 10, F10D13.2, F10D13_2}, CLE9 (CLAVATA3/ESR-RELATED 9) [NCBI Gene 839200] {aka CLAVATA3/ESR-RELATED 9, T1K7.3, T1K7_3}, CLE13 (CLAVATA3/ESR-RELATED 13) [NCBI Gene 843734] {aka CLAVATA3/ESR-RELATED 13}, BOP2 (Ankyrin repeat family protein / BTB/POZ domain-containing protein) [NCBI Gene 818735] {aka BLADE ON PETIOLE2, F13H10.8, F13H10_8}, HAM1 (histone acetyltransferase of the MYST family 1) [NCBI Gene 836582] {aka MUB3.13, MUB3_13, histone acetyltransferase of the MYST family 1}, KNAT6 (homeobox protein knotted-1-like 6) [NCBI Gene 838946] {aka F26F24.32, F26F24_32, KNAT6L, KNAT6S, KNOTTED1-like homeobox gene 6}, WOX4 (WUSCHEL related homeobox 4) [NCBI Gene 841113] {aka F2G19.11, F2G19_11, WUSCHEL related homeobox 4}, KAPP (kinase associated protein phosphatase) [NCBI Gene 832048] {aka RAG1, ROOT ATTENUATED GROWTH 1, T24G5.3, kinase associated protein phosphatase}, EBF2 (EIN3-binding F box protein 2) [NCBI Gene 832607] {aka EIN3-binding F box protein 2, F18G18.90, F18G18_90}, BAM2 (beta-amylase 2) [NCBI Gene 827959] {aka BETA-AMYLASE 9, BMY9, F6N23.1, F6N23_1, beta-amylase 2}, PRS (Homeodomain-like superfamily protein) [NCBI Gene 817410] {aka PRESSED FLOWER, PRESSED FLOWER 1, PRS1, T8O18.10, T8O18_10, WOX3}, CLE22 (CLAVATA3/ESR-RELATED 22) [NCBI Gene 831098] {aka CLAVATA3/ESR-RELATED 22}, WUS (Homeodomain-like superfamily protein) [NCBI Gene 816305] {aka PGA6, T27K22.18, T27K22_18, WUS1, WUSCHEL, WUSCHEL 1}, HSL1 (HSI2-like 1) [NCBI Gene 829332] {aka F10N7.180, F10N7_180, HSI2-L1, HSI2-like 1, VAL2, VP1/ABI3-LIKE 2}, CLV1 (Leucine-rich receptor-like protein kinase family protein) [NCBI Gene 843915] {aka ATCLV1, CLAVATA 1, CLV1 RECEPTOR KINASE PRECURSOR, FAS3, FASCIATA 3, FLO5}, EBF1 (EIN3-binding F box protein 1) [NCBI Gene 817087] {aka EIN3-binding F box protein 1, F13B15.15, F13B15_15, FBL6}, AS2 (Lateral organ boundaries (LOB) domain family protein) [NCBI Gene 842873] {aka ASYMMETRIC LEAVES 2, F5I14.15, F5I14_15}, CLE12 (CLAVATA3/ESR-RELATED 12) [NCBI Gene 843211] {aka CLAVATA3/ESR-RELATED 12}
- **Diseases:** SYNTHASE (MESH:D020159), injury to (MESH:D014947), SAM (MESH:D010485), RM (MESH:C537613), CLV3 deficiency (MESH:D007153), CLE (MESH:D020964), SE precursor cell (SPC) receptor-like protein (MESH:D054218)
- **Chemicals:** carbon (MESH:D002244), ethylene (MESH:C036216), nitrogen (MESH:D009584), sucrose (MESH:D013395), Poly-Q (MESH:C097188), Auxin (MESH:D007210), ROS (-)
- **Species:** Populus deltoides (species) [taxon 3696], Prunus persica (peach, species) [taxon 3760], Picea abies (Norway spruce, species) [taxon 3329], Amborella trichopoda (species) [taxon 13333], Physcomitrium patens (species) [taxon 3218], Oryza sativa (Asian cultivated rice, species) [taxon 4530], Solanum tuberosum (potatoes, species) [taxon 4113], Bryophyta (mosses, clade) [taxon 3208], Selaginella moellendorffii (species) [taxon 88036], Populus trichocarpa (black cottonwood, species) [taxon 3694], Polypodiopsida (ferns, class) [taxon 241806], Arabidopsis thaliana (mouse-ear cress, species) [taxon 3702], Solanum lycopersicum (tomato, species) [taxon 4081], Camellia oleifera (tea-oil Camellia, species) [taxon 385388], Homo sapiens (human, species) [taxon 9606], Zea mays (maize, species) [taxon 4577]

## Full text

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## Figures

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## References

171 references — full list in the complete paper: https://tomesphere.com/paper/PMC12114883/full.md

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Source: https://tomesphere.com/paper/PMC12114883