# Comparative proteomic profiling of receptor kinase signaling reveals key trafficking components enforcing plant stomatal development

**Authors:** Pengfei Bai, Minh Huy Vu, Chiaki Komatsu, Ophelia Papoulas, Kazuo Ebine, Akira Nozawa, Tatsuya Sawasaki, Takashi Ueda, Edward M. Marcotte, Keiko U. Torii

PMC · DOI: 10.1126/sciadv.aeb6464 · 2026-03-25

## TL;DR

This study maps the proteins involved in receptor kinase signaling during plant stomatal development, highlighting the role of endocytosis in regulating this process.

## Contribution

The study identifies specific endocytosis components that regulate ERECTA receptor kinase internalization during stomatal development.

## Key findings

- ERECTA interacts with TOO MANY MOUTHS and endosomal trafficking machinery via clathrin-mediated endocytosis.
- PICALM subfamily proteins synergistically regulate ERECTA internalization and stomatal patterning.
- Disruption of PICALMs impairs ERECTA endocytosis and leads to stomatal clustering.

## Abstract

Receptor kinases are pivotal for growth, development, and environmental response of plants. Yet, their regulatory mechanisms and spatial dynamics remain underexplored. The ERECTA-family receptor kinases coordinate diverse developmental processes, including stomatal development. To understand the proteomic landscape of the ERECTA-mediated signaling pathways, we report comparative analyses of the ERECTA interactome and proximitome by epitope-tagged affinity-purification (ET-AP) and TurboID-based proximity labeling (TbID-PL) mass spectrometry, respectively. While ET-AP recovered receptor complex components (e.g., TOO MANY MOUTHS), TbID-PL effectively captured transient associations with the components of endosomal trafficking, i.e., clathrin-mediated endocytosis machinery. We further identify that specific subfamily members of phosphatidylinositol-binding clathrin assembly proteins (PICALMs) interact with and synergistically regulate ERECTA internalization. Mutations in PICALMs impair ERECTA endocytosis and lead to excessive stomatal clustering by dampening the downstream signaling output. Together, we provide a proteomic atlas of the ERECTA signaling network and demonstrate that timely removal of receptor kinase by the endocytosis machinery is essential for active signal transduction enforcing stomatal patterning.

Proteomic mapping uncovers endocytosis adaptors that drive receptor internalization for robust stomatal development.

## Linked entities

- **Genes:** ER (Leucine-rich receptor-like protein kinase family protein) [NCBI Gene 817173], TMM (Leucine-rich repeat (LRR) family protein) [NCBI Gene 844348], picalm.S (phosphatidylinositol binding clathrin assembly protein S homeolog) [NCBI Gene 108710036]
- **Proteins:** ER (Leucine-rich receptor-like protein kinase family protein), TMM (Leucine-rich repeat (LRR) family protein), picalm.S (phosphatidylinositol binding clathrin assembly protein S homeolog), cltc.L (clathrin, heavy chain (Hc) L homeolog)

## Full-text entities

- **Genes:** BAK1 (BRI1-associated receptor kinase) [NCBI Gene 829480] {aka ATBAK1, ATSERK3, BRI1-associated receptor kinase, ELG, ELONGATED, F17M5.190}, ACT2 (actin 2) [NCBI Gene 821411] {aka DEFORMED ROOT HAIRS 1, DER1, ENHANCER OF LRX1 2, ENL2, FIZ2, FRIZZY AND KINKED SHOOTS 2}, MPK1 (mitogen-activated protein kinase 1) [NCBI Gene 837559] {aka ATMPK1, F14N23.9, F14N23_9, MITOGEN-ACTIVATED PROTEIN KINASE, mitogen-activated protein kinase 1}, STOMAGEN (stomagen) [NCBI Gene 826909] {aka EPFL9, F25G13.60, F25G13_60}, ERL2 (ERECTA-like 2) [NCBI Gene 830609] {aka ERECTA-like 2, T28J14.120, T28J14_120}, EPF2 (Putative membrane lipoprotein) [NCBI Gene 840324] {aka EPIDERMAL PATTERNING FACTOR 2}, PHOT1 (phototropin 1) [NCBI Gene 823721] {aka F16L2.3, JK224, NONPHOTOTROPIC HYPOCOTYL 1, NPH1, PHOTOTROPIN, ROOT PHOTOTROPISM 1}, TMM (Leucine-rich repeat (LRR) family protein) [NCBI Gene 844348] {aka AtRLP17, F18B13.16, F18B13_16, Receptor Like Protein 17, TOO MANY MOUTHS}, ER (Leucine-rich receptor-like protein kinase family protein) [NCBI Gene 817173] {aka ERECTA, QRP1, QUANTITATIVE RESISTANCE TO PLECTOSPHAERELLA 1, T1D16.3, T1D16_3}, BRI1 (Leucine-rich receptor-like protein kinase family protein) [NCBI Gene 830095] {aka ATBRI1, BIN1, BR INSENSITIVE 1, BRASSINOSTEROID INSENSITIVE 1, CABBAGE 2, CBB2}, YKT6 (YKT6 vesicular SNARE protein) [NCBI Gene 10652], AN (NAD(P)-binding Rossmann-fold superfamily protein) [NCBI Gene 839401] {aka ANGUSTIFOLIA, DETORQUEO, DOQ, F22L4.6, F22L4_6}, GABRA1 (gamma-aminobutyric acid type A receptor subunit alpha1) [NCBI Gene 2554] {aka DEE19, ECA4, EIEE19, EJM, EJM5}, ATERDJ3B (DNAJ heat shock family protein) [NCBI Gene 825434] {aka ERDJ3B}, PICALM (phosphatidylinositol binding clathrin assembly protein) [NCBI Gene 8301] {aka CALM, CLTH, LAP}, EPF1 (epidermal patterning factor 1) [NCBI Gene 816621] {aka EPIDERMAL PATTERNING FACTOR 1}, HAE (Leucine-rich receptor-like protein kinase family protein) [NCBI Gene 828967] {aka F20O9.180, F20O9_180, HAESA, RECEPTOR-LIKE PROTEIN KINASE 5, RLK5}, SPCH (basic helix-loop-helix (bHLH) DNA-binding superfamily protein) [NCBI Gene 835402] {aka MFH8.15, SPEECHLESS}, Kin3 (Protein kinase superfamily protein) [NCBI Gene 816227] {aka T23A1.8, T23A1_8, kinase 3}, SDF2 (stromal cell-derived factor 2-like protein precursor) [NCBI Gene 817049] {aka ATSDF2-LIKE, ATSDL, Arabidopsis thaliana STROMAL CELL-DERIVED FACTOR 2-like protein precursor, AtSDF2, F13D4.70, F13D4_70}, TFAP2A (transcription factor AP-2 alpha) [NCBI Gene 7020] {aka AP-2, AP-2alpha, AP2TF, BOFS, TFAP2}, ERL1 (ERECTA-like 1) [NCBI Gene 836344] {aka ERECTA-like 1, MMI9.14, MMI9_14}, MAP2K4 (mitogen-activated protein kinase kinase 4) [NCBI Gene 6416] {aka JNKK, JNKK1, MAPKK4, MEK4, MKK4, PRKMK4}, AT3G14840 (Leucine-rich repeat transmembrane protein kinase) [NCBI Gene 820713] {aka LIK1, LysM RLK1-interacting kinase 1}, SNAP91 (synaptosome associated protein 91) [NCBI Gene 9892] {aka AP180, CALM}, YDA (Protein kinase superfamily protein) [NCBI Gene 842674] {aka EMB71, EMBRYO DEFECTIVE 71, F24D7.11, F24D7_11, MAP KINASE KINASE KINASE 4, MAPKKK4}, FLS2 (Leucine-rich receptor-like protein kinase family protein) [NCBI Gene 834676] {aka FLAGELLIN-SENSITIVE 2, MPL12.13, MPL12.8, MPL12_13}, BSK2 (BR-signaling kinase 2) [NCBI Gene 834700] {aka BR-signaling kinase 2, F10E10.4, F10E10_4, brassinosteroid-signaling kinase 2}, ARA7 (Ras-related small GTP-binding family protein) [NCBI Gene 827706] {aka ARA-7, ARABIDOPSIS RAB GTPASE HOMOLOG F2B, ATRAB-F2B, ATRAB5B, ATRABF2B, F24J7.190}, FPR2 (formyl peptide receptor 2) [NCBI Gene 2358] {aka ALX, ALXR, FMLP-R-II, FMLPX, FPR2A, FPRH1}, HERK1 (hercules receptor kinase 1) [NCBI Gene 823774] {aka hercules receptor kinase 1}, NPH4 (Transcriptional factor B3 family protein / auxin-responsive factor AUX/IAA-like protein) [NCBI Gene 832196] {aka ARF7, AUXIN RESPONSE FACTOR 7, AUXIN-REGULATED TRANSCRIPTIONAL ACTIVATOR 7, AUXIN-RESPONSIVE TRANSCRIPTIONAL ACTIVATOR 7, BIP, BIPOSTO}, HSL1 (HSI2-like 1) [NCBI Gene 829332] {aka F10N7.180, F10N7_180, HSI2-L1, HSI2-like 1, VAL2, VP1/ABI3-LIKE 2}, BSK1 (BR-signaling kinase 1) [NCBI Gene 829676] {aka BR-signaling kinase 1, F23E12.210, F23E12_210, brassinosteroid-signaling kinase 1}, PIN3 (Auxin efflux carrier family protein) [NCBI Gene 843432] {aka ARABIDOPSIS PIN-FORMED 3, ATPIN3, F15H11.14, F15H11_14, PIN-FORMED 3}, PICALM (phosphatidylinositol binding clathrin assembly protein) [NCBI Gene 513579], PIN7 (Auxin efflux carrier family protein) [NCBI Gene 838916] {aka ARABIDOPSIS PIN-FORMED 7, ATPIN7, PIN-FORMED 7, T26J12.14, T26J12_14}
- **Diseases:** GMC (MESH:D002292), dwarf (MESH:D004393), developmental (MESH:C567924), TbID-PL (MESH:D019292), SOMATIC (MESH:D013001)
- **Chemicals:** BFA (MESH:D020126), Tween 20 (MESH:D011136), iodoacetamide (MESH:D007460), ATP (MESH:D000255), sucrose (MESH:D013395), formic acid (MESH:C030544), MES (MESH:C004550), NaCl (MESH:D012965), glucose (MESH:D005947), urea (MESH:D014508), nitrogen (MESH:D009584), ABA (MESH:D000040), polyacrylamide (MESH:C016679), FM4-64 (MESH:C092350), glycine (MESH:D005998), DTT (MESH:D004229), Laemmli buffer (MESH:C088816), water (MESH:D014867), cycloheximide (MESH:D003513), acetonitrile (MESH:C032159), STOP (MESH:D014002), cysteine (MESH:D003545), Na2CO3 (MESH:C005686), sodium fluoride (MESH:D012969), SA (MESH:D000077145), DMSO (MESH:D004121), oil (MESH:D009821), carbamidomethyl cysteine (MESH:C034636), AP (MESH:D000667), propidium iodide (MESH:D011419), SDS (MESH:D012967), MgCl2 (MESH:D015636), TOPO (MESH:C044965), Tris(2-carboxyethyl) phosphine (MESH:C080938), sodium hypochlorite (MESH:D012973), agar (MESH:D000362), EDTA (MESH:D004492), Ponceau S (MESH:C032756), mannitol (MESH:D008353), biotin (MESH:D001710), CaCl2 (MESH:D002122), glycerol (MESH:D005990), C4859 (-), agarose (MESH:D012685), Concanamycin A (MESH:C036978), polyvinylidene difluoride (MESH:C024865), phenylmethylsulfonyl fluoride (MESH:D010664), disulfide (MESH:D004220), KCl (MESH:D011189), Wm (MESH:D000077191), auxin (MESH:D007210), Triton X-100 (MESH:D017830), sodium molybdate (MESH:C024687), ethanol (MESH:D000431), trifluoroethanol (MESH:D014270), methionine (MESH:D008715)
- **Species:** Rattus norvegicus (brown rat, species) [taxon 10116], Agrobacterium tumefaciens (species) [taxon 358], Homo sapiens (human, species) [taxon 9606], Mus musculus (house mouse, species) [taxon 10090], Arabidopsis thaliana (mouse-ear cress, species) [taxon 3702]
- **Cell lines:** Col-0 — Homo sapiens (Human), Familial hypertrophic cardiomyopathy type 26, Induced pluripotent stem cell (CVCL_A6XE), ES9-17 — Mus musculus (Mouse), Hybridoma (CVCL_C5MM)

## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC13015889/full.md

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Source: https://tomesphere.com/paper/PMC13015889