Stomatal lineage progression and spacing (EPF-ERECTA-YODA-MAPK and SPCH/MUTE/FAMA-SCRM)

In the Arabidopsis leaf epidermis, stomata are produced by a dedicated cell lineage whose successive transitions are driven by three closely related group Ia bHLH transcription factors, each acting as a heterodimer with the broadly expressed group IIIb bHLHs SCREAM/ICE1 (SCRM) and SCRM2. SPEECHLESS (SPCH) initiates the lineage by driving the asymmetric entry division of a meristemoid mother cell, MUTE terminates the self-renewing asymmetric divisions of the meristemoid and converts it into a guard mother cell (GMC), and FAMA drives the single symmetric GMC division and guard cell differentiation, then locks in guard cell fate with RETINOBLASTOMA-RELATED. Lineage entry and spacing are restrained by cell-cell signalling: the secreted cysteine-rich peptide EPF2, produced by early lineage cells, binds the leucine-rich-repeat receptor kinase ERECTA in a complex with the non-catalytic co-receptor TOO MANY MOUTHS (TMM); ligand binding recruits SERK co-receptor kinases and activates the MAPKKK YODA, which phosphorylates MKK4/MKK5, which in turn activate MPK3/MPK6. MPK3/MPK6, docked onto SCRM through its KiDoK motif and recruited with YODA to the cortex by the polarity scaffold BASL, phosphorylate SPCH and SCRM and promote their degradation, limiting lineage entry. Because SPCH-SCRM directly activates EPF2 and TMM, the circuit forms a negative feedback loop that self-organizes stomatal density and the one-cell spacing rule. The related peptide EPF1, perceived mainly by ERL1, acts later on spacing divisions, and the positive peptide stomagen (EPFL9) competes with EPF2 for ERECTA-TMM. Brassinosteroid (via BIN2 inhibition of YODA), CO2 (via CRSP cleavage of EPF2) and other environmental inputs converge on this module.

MODULE:stomatal_lineage_developmentDRAFTCONCRETEDevelopmental Processmodules/stomatal_lineage_development.yaml
stomatal complex developmentGO:0010374 stomatal lineage progressionGO:0010440 stomatal complex patterningGO:0010375
PMID:18641265
SCREAM/ICE1 and SCREAM2 specify three cell-state transitional steps leading to arabidopsis stomatal differentiation.
SPCH, MUTE and FAMA act as heterodimers with SCRM/ICE1 and SCRM2 at three successive steps.
Here, we identify two paralogous proteins, SCREAM (SCRM) and SCRM2, which directly interact with and specify the sequential actions of SPCH, MUTE, and FAMA.
PMID:17183267
Termination of asymmetric cell division and differentiation of stomata.
SPCH, MUTE and FAMA control stomatal development at three consecutive steps.
Together, SPCH, MUTE and FAMA bHLH proteins control stomatal development at three consecutive steps
PMID:22241782
Direct interaction of ligand-receptor pairs specifying stomatal patterning.
ERECTA-family receptors are the primary EPF receptors; EPF2-ERECTA specifies lineage entry and TMM modulates the signal.
Our results place the ERECTA family as the primary receptors for EPFs with TMM as a signal modulator and establish EPF2-ERECTA and EPF1-ERL1 as ligand-receptor pairs specifying two steps of stomatal development
PMID:17259259
Stomatal development and patterning are regulated by environmentally responsive mitogen-activated protein kinases in Arabidopsis.
MKK4/MKK5-MPK3/MPK6 act downstream of YODA in stomatal development.
We further establish that the MKK4/MKK5-MPK3/MPK6 module is downstream of YODA, a MAPKKK.
PMID:26203655
Molecular Framework of a Regulatory Circuit Initiating Two-Dimensional Spatial Patterning of Stomatal Lineage.
SPCH-SCRM directly activates EPF2 and TMM, closing a negative feedback loop.
This transcription factor module directly binds to the promoters and activates a secreted signal, EPIDERMAL PATTERNING FACTOR2, and the receptor modifier TOO MANY MOUTHS, while the receptor ERECTA lies outside of this module.

Boundary: the module covers the core EPF2-ERECTA/TMM-YODA-MKK4/5-MPK3/6 inhibitory relay and the SPCH-MUTE-FAMA/SCRM transcriptional switch of the Arabidopsis stomatal lineage. Parallel or modulatory components are described in prose but not modelled as annotons because they lack gene reviews in this repository: EPF1 and ERL1/ERL2 (spacing divisions), stomagen/EPFL9 (antagonist ligand), SERK co-receptors, BASL/POLAR polarity scaffolds, BIN2, CRSP, SCRM2 and MPK3 (MPK3 is named in prose as MPK6's redundant partner). MKK4 and MKK5 are grounded as representative members of the redundant MAPKK step and both have complete gene reviews. Annoton molecular functions follow the gene reviews' core_functions (EPF2, TMM, ERECTA, YDA, MKK4, MKK5, MPK6, SPCH, MUTE, FAMA, ICE1). No production GO-CAM in gocams/index.tsv contains any member, so no gocam_associations are given. No PANTHER family ids are asserted (families are described by preferred_term and representative members only). Deep research by the Falcon provider was unavailable (HTTP 402) during this session.

11Nodes
10Parts
0Variant Sets
0Variants
10Annotons
8Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:stomatal_lineage_development deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

11 gene-function check(s) reflected in core functions · 0 conflict(s) · 1 evidence or coverage gap(s) (12 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
epf2_ligand EPF2
UniProtKB:Q8LC53
Gene
receptor ligand activity
GO:0048018
Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
erecta_receptor ERECTA
UniProtKB:Q42371
Gene
transmembrane receptor protein serine/threonine kinase activity
GO:0004675
Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
tmm_coreceptor TMM
UniProtKB:Q9SSD1
Gene
coreceptor activity
GO:0015026
Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
yda_mapkkk YDA (YODA)
UniProtKB:Q9CAD5
Gene
MAP kinase kinase kinase activity
GO:0004709
Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mkk4_mkk5_activity MKK4
UniProtKB:O80397
Family Representative
MAP kinase kinase activity
GO:0004708
Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mkk4_mkk5_activity MKK5
UniProtKB:Q8RXG3
Family Representative
MAP kinase kinase activity
GO:0004708
Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mpk6_mapk MPK6
UniProtKB:Q39026
Gene
MAP kinase activity
GO:0004707
Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ice1_partner ICE1 (SCRM)
UniProtKB:Q9LSE2
Gene
protein heterodimerization activity
GO:0046982
Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
spch_tf SPCH
UniProtKB:Q700C7
Gene
DNA-binding transcription activator activity
GO:0001216
Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mute_tf MUTE
UniProtKB:Q9M8K6
Gene
DNA-binding transcription factor activity
GO:0003700
Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fama_tf FAMA
UniProtKB:Q56YJ8
Gene
DNA-binding transcription factor activity
GO:0003700
Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mkk4_mkk5_activity MKK4/MKK5 group C MAP kinase kinases
Family
MAP kinase kinase activity
GO:0004708
Family Id Missing
The family has no identifier linking it to a curated family review.

Feedback loops (advisory, prose-driven: a regulator counts as "feedback" when its own description says so)

✓ every negative regulator described as feedback has an upstream edge closing the loop.

  • yoda_mapk_cascade ⊣ spch_entry [closed]
    yoda_mapk_cascade is regulated by epf2_erecta_tmm_perception: feedback loop closed

Gene-review completeness (11/11 grounded genes reviewed)

10 complete review(s) · 5 with deep research · 0 missing review · 6 reviewed but lacking deep research

Gene Review Complete Deep research
EPF2 Q8LC53 ✓ ✓ ✗
ERECTA Q42371 ✓ ✓ ✗
FAMA Q56YJ8 ✓ ✓ ✗
ICE1 Q9LSE2 ✓ ✓ ✗
MKK4 O80397 ✓ 40/41 ✓
MKK5 Q8RXG3 ✓ ✓ ✓
MPK6 Q39026 ✓ ✓ ✓
MUTE Q9M8K6 ✓ ✓ ✓
SPCH Q700C7 ✓ ✓ ✓
TMM Q9SSD1 ✓ ✓ ✗
YDA Q9CAD5 ✓ ✓ ✗

Details

Context
Arabidopsis thalianaNCBITaxon:3702
extracellular regionGO:0005576 plasma membraneGO:0005886 cell cortexGO:0005938 nucleusGO:0005634
Stomatal lineage progression and spacingDevelopmental Processstomatal_lineage_development

EPF2 peptide signalling through ERECTA/TMM and the YODA-MKK4/5-MPK3/6 cascade restrains the SPCH-SCRM lineage-entry factor, while SPCH, MUTE and FAMA (each heterodimerized with SCRM) drive the successive stomatal lineage transitions.

stomatal complex developmentGO:0010374 stomatal lineage progressionGO:0010440 stomatal complex patterningGO:0010375
Context
Arabidopsis thalianaNCBITaxon:3702
extracellular regionGO:0005576 plasma membraneGO:0005886 cell cortexGO:0005938 nucleusGO:0005634

Connections

EPF2 binding to ERECTA-TMM (with SERKs) activates the YODA-MKK4/5-MPK3/6 cascade.
PMID:26083750
Application of MEPF2 peptides to Arabidopsis wild-type seedlings rapidly elicited phosphorylation of MPK3 and MPK6 in 10 min, a characteristic signature of MAPK activation
yoda_mapk_cascade -> spch_entry Negatively Regulates
MPK3/MPK6, docked on SCRM, phosphorylate SPCH (and SCRM) and promote their degradation, limiting stomatal lineage entry.
PMID:25843888
Activated MPK3/6 reinforces the feedback loop by phosphorylating BASL and inhibits stomatal fate by phosphorylating SPCH.
spch_entry -> epf2_erecta_tmm_perception Positively Regulates
Negative feedback loop - SPCH-SCRM directly activates EPF2 and TMM transcription, so lineage entry generates the inhibitory signal for neighbouring cells.
PMID:26203655
This transcription factor module directly binds to the promoters and activates a secreted signal, EPIDERMAL PATTERNING FACTOR2, and the receptor modifier TOO MANY MOUTHS
Part 1: peptide ligand perception at the cell surface
EPF2 perception by the ERECTA-TMM receptor complexRegulatory Stepepf2_erecta_tmm_perception

Secreted EPF2 binds the ERECTA ectodomain in a constitutive complex with the co-receptor TMM, activating ERECTA kinase signalling.

Annotons

EPF2: inhibitory peptide ligand
epf2_ligand
Participant: Gene Product: EPF2
Gene Product:

Function

receptor ligand activityGO:0048018

Processes

negative regulation of stomatal complex developmentGO:2000122

Locations

extracellular regionGO:0005576

Produced by meristemoid mother cells and early lineage cells; inhibits neighbouring protodermal cells from adopting MMC fate.

PMID:26083750
EPF2 directly binds ERECTA and TMM and elicits rapid MPK3/6 phosphorylation.
Both EPF2 and Stomagen directly bind to ER and its co-receptor TOO MANY MOUTHS.
file:ARATH/EPF2/EPF2-ai-review.yaml
Gene review core function receptor ligand activity in negative regulation of stomatal complex development.
ERECTA: LRR receptor kinase
erecta_receptor
Participant: Gene Product: ERECTA
Gene Product:

Function

transmembrane receptor protein serine/threonine kinase activityGO:0004675

Processes

negative regulation of stomatal complex developmentGO:2000122

Locations

plasma membraneGO:0005886

Principal EPF2 receptor; recruits SERK co-receptor kinases and relays the signal to YODA. Paralogs ERL1/ERL2 perceive EPF1 at later spacing divisions.

PMID:26320950
EPF ligands induce ERECTA-SERK heteromerization and SERKs act upstream of the MAPK cascade.
SERK family RLKs regulate stomatal patterning downstream of EPF ligands and upstream of a MAP kinase cascade
file:ARATH/ERECTA/ERECTA-ai-review.yaml
Gene review core function.
TMM: non-catalytic LRR co-receptor
tmm_coreceptor
Participant: Gene Product: TMM
Gene Product:

Function

coreceptor activityGO:0015026

Processes

stomatal complex patterningGO:0010375

Locations

plasma membraneGO:0005886

Forms constitutive complexes with ERECTA/ERL1 that create the EPF1/EPF2 binding pocket and exclude EPFL4/6, acting as a ligand-specificity switch.

PMID:28536146
TMM-ERf complexes are the receptors of EPF1 and EPF2.
TMM interaction with ERL1 creates a binding pocket for recognition of EPF1 and EPF2, indicating that the constitutive TMM-ERf complexes function as the receptors of EPF1 and EPF2.
file:ARATH/TMM/TMM-ai-review.yaml
Gene review core function.
Part 2: MAP kinase relay
YODA-MKK4/5-MPK3/6 MAP kinase cascadeSignaling Pathwayyoda_mapk_cascade

The MAPKKK YODA activates the redundant MAPKKs MKK4/MKK5, which activate the redundant MAPKs MPK3/MPK6; BASL concentrates YODA and MPK3/6 at the cortex of asymmetrically dividing cells.

MAPK cascadeGO:0000165

Connections

yoda_mapkkk -> mkk4_mkk5_mapkk Positively Regulates
YODA phosphorylates and activates MKK4/MKK5.
PMID:17259259
We further establish that the MKK4/MKK5-MPK3/MPK6 module is downstream of YODA, a MAPKKK.
PMID:22307275
BIN2 phosphorylates YDA to inhibit YDA phosphorylation of its substrate MKK4
mkk4_mkk5_mapkk -> mpk3_mpk6_mapk Positively Regulates
MKK4/MKK5 phosphorylate and activate MPK3/MPK6.
PMID:17259259
We further establish that the MKK4/MKK5-MPK3/MPK6 module is downstream of YODA, a MAPKKK.
Part 1: MAPKKK
YODA MAP kinase kinase kinaseRegulatory Stepyoda_mapkkk

Annotons

YDA: MAP kinase kinase kinase
yda_mapkkk
Participant: Gene Product: YDA (YODA)
Gene Product:
YDA (YODA)UniProtKB:Q9CAD5

Function

MAP kinase kinase kinase activityGO:0004709

Processes

MAPK cascadeGO:0000165 negative regulation of stomatal complex developmentGO:2000122

Locations

cell cortexGO:0005938
PMID:15178800
YODA loss gives excess stomata; constitutive YODA eliminates stomata.
Null mutations in YODA lead to excess stomata, whereas constitutive activation of YODA eliminated stomata.
file:ARATH/YDA/YDA-ai-review.yaml
Gene review core function.
Part 2: MAPKK
MKK4/MKK5 MAP kinase kinasesRegulatory Stepmkk4_mkk5_mapkk

Annotons

MKK4/MKK5: MAP kinase kinase (redundant pair)
mkk4_mkk5_activity
Participant: Family: MKK4/MKK5 group C MAP kinase kinases
Family:
MKK4/MKK5 group C MAP kinase kinases
Representative Members: MKK4UniProtKB:O80397 MKK5UniProtKB:Q8RXG3

Function

MAP kinase kinase activityGO:0004708

Processes

MAPK cascadeGO:0000165 negative regulation of stomatal complex developmentGO:2000122

Phosphorylated by YODA; activate MPK3/MPK6. Loss of MKK4/MKK5 causes stomatal clustering.

PMID:17259259
MKK4/MKK5 and MPK3/MPK6 regulate stomatal development downstream of YODA.
Loss of function of MKK4/MKK5 or MPK3/MPK6 disrupts the coordinated cell fate specification of stomata versus pavement cells, resulting in the formation of clustered stomata.
PMID:22307275
YDA phosphorylates MKK4.
BIN2 phosphorylates YDA to inhibit YDA phosphorylation of its substrate MKK4
Part 3: MAPK
MPK3/MPK6 MAP kinasesRegulatory Stepmpk3_mpk6_mapk

Annotons

MPK6 (with MPK3): MAP kinase
mpk6_mapk
Participant: Gene Product: MPK6
Gene Product:

Function

MAP kinase activityGO:0004707

Processes

MAPK cascadeGO:0000165

Locations

nucleusGO:0005634 cell cortexGO:0005938

Acts redundantly with MPK3 (UniProtKB:Q39023); phosphorylates SPCH and SCRM in the nucleus (docked on SCRM's KiDoK motif) and BASL at the cortex.

PMID:19008449
SPCH is a MAPK phosphorylation target.
We found that a unique domain in a basic helix-loop-helix (bHLH) stomatal initiating factor, SPEECHLESS, renders it a MAPK phosphorylation target in vitro and modulates its function in vivo.
file:ARATH/MPK6/MPK6-ai-review.yaml
Gene review core function MAP kinase activity.
Part 3: bHLH transcriptional switch of the stomatal lineage
SPCH, MUTE and FAMA heterodimers with SCRM/ICE1Regulatory Stepbhlh_lineage_switch

Stage-specific group Ia bHLHs heterodimerize with SCRM/ICE1 (or SCRM2) to drive lineage entry (SPCH), meristemoid-to-GMC transition (MUTE) and guard cell differentiation (FAMA).

Connections

SPCH-initiated meristemoids later express MUTE, which terminates their asymmetric divisions.
MUTE-specified GMCs express FAMA, which drives the symmetric division and guard cell differentiation.
scrm_partner -> spch_entry Positively Regulates
SCRM/SCRM2 heterodimerize with SPCH (and likewise MUTE and FAMA) and are required for each transition.
PMID:18641265
successive loss of SCRM and SCRM2 recapitulated the phenotypes of fama, mute, and spch
Part 1: shared heterodimer partner and MAPK scaffold
SCRM/ICE1 common bHLH partnerRegulatory Stepscrm_partner

Annotons

ICE1/SCRM: heterodimer partner of SPCH, MUTE and FAMA
ice1_partner
Participant: Gene Product: ICE1 (SCRM)
Gene Product:
ICE1 (SCRM)UniProtKB:Q9LSE2

Function

protein heterodimerization activityGO:0046982

Processes

stomatal lineage progressionGO:0010440

Locations

nucleusGO:0005634

Redundant with SCRM2; also scaffolds MPK3/MPK6 to SPCH through its KiDoK motif (protein-macromolecule adaptor activity), coupling the MAPK cascade to lineage-entry control.

PMID:31235876
SCRM is a scaffold that recruits MPK3/6 to SPCH.
here, we report that the basic helix-loop-helix protein SCREAM functions as a scaffold that recruits MPK3/6 to downregulate SPEECHLESS, a transcription factor that initiates stomatal cell lineages.
file:ARATH/ICE1/ICE1-ai-review.yaml
Gene review core functions (heterodimerization, DNA-binding TF, adaptor).
Part 2: lineage entry and asymmetric division
SPCH-driven lineage entryRegulatory Stepspch_entry

Annotons

SPCH: lineage-initiating bHLH activator
spch_tf
Participant: Gene Product: SPCH
Gene Product:

Function

DNA-binding transcription activator activityGO:0001216

Processes

regulation of stomatal complex developmentGO:2000038

Locations

nucleusGO:0005634

Initiates the stomatal lineage by directing the asymmetric entry division; directly activates EPF2, TMM and SCRM (feedback); phosphorylated and destabilized by MPK3/MPK6.

PMID:17183267
SPCH directs the first asymmetric division.
We show that SPCH directs the first asymmetric division that initiates stomatal lineage.
file:ARATH/SPCH/SPCH-ai-review.yaml
Gene review core function (read-only member for this module).
Part 3: meristemoid to guard mother cell transition
MUTE-driven meristemoid-to-GMC transitionRegulatory Stepmute_transition

Annotons

MUTE: terminates meristemoid divisions
mute_tf
Participant: Gene Product: MUTE
Gene Product:

Function

DNA-binding transcription factor activityGO:0003700

Processes

stomatal complex developmentGO:0010374

Locations

nucleusGO:0005634
PMID:17183267
MUTE is the switch for meristemoid fate transition.
Here we report that the Arabidopsis thaliana basic helix-loop-helix (bHLH) protein MUTE is a key switch for meristemoid fate transition.
file:ARATH/MUTE/MUTE-ai-review.yaml
Gene review core function (read-only member for this module).
Part 4: guard cell differentiation and fate commitment
FAMA-driven guard cell differentiationRegulatory Stepfama_differentiation

Annotons

FAMA: terminal guard cell differentiation factor
fama_tf
Participant: Gene Product: FAMA
Gene Product:

Function

DNA-binding transcription factor activityGO:0003700

Processes

guard cell differentiationGO:0010052

Locations

nucleusGO:0005634

Drives guard cell differentiation and halts GMC divisions; recruits RBR via an LxCxE motif to make guard cell fate irreversible.

PMID:17088607
FAMA promotes guard cell differentiation and halts precursor proliferation.
FAMA is a putative basic helix-loop-helix transcription factor whose activity is required to promote differentiation of stomatal guard cells and to halt proliferative divisions in their immediate precursors.
file:ARATH/FAMA/FAMA-ai-review.yaml
Gene review core function.