CLV1

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0007172 signal complex assembly	IDA PMID:10072399 The CLAVATA1 receptor-like kinase requires CLAVATA3 for its ...	ACCEPT	Summary: CLV1 is experimentally observed in 185-kD and CLV3-dependent 450-kD receptor complexes; the 450-kD complex includes KAPP and a Rho GTPase-related protein. This directly supports signal complex assembly as part of the CLV3-CLV1 signaling mechanism. Reason: The term captures a specific mechanistic event in CLV1 signaling rather than a downstream developmental phenotype. Supporting Evidence: PMID:10072399 CLV1 is present in two protein complexes in vivo. One is approximately 185 kD, and the other is approximately 450 kD. PMID:10072399 CLV3 functions to promote the assembly of the active 450-kD complex, which then relays signal transduction through a Rho GTPase.
GO:0009934 regulation of meristem structural organization	IMP PMID:9160749 The CLAVATA1 gene encodes a putative receptor kinase that co...	ACCEPT	Summary: Loss of CLV1 causes Arabidopsis shoot and floral meristems to accumulate excess undifferentiated cells. This is the canonical biological process regulated by CLV1 and is supported by mutant phenotype and expression data. Reason: This is a core biological role of CLV1 in maintaining meristem size and organization through CLV3/CLE receptor signaling. Supporting Evidence: PMID:9160749 Arabidopsis plants homozygous for mutations at the CLAVATA1 (CLV1) locus accumulate excess undifferentiated cells. PMID:9160749 CLV1 expression in the inflorescence is specifically associated with meristematic activity. file:ARATH/CLV1/CLV1-deep-research-falcon.md CLV1 (Q9SYQ8) is best annotated as a plasma-membrane LRR receptor Ser/Thr kinase
GO:0030154 cell differentiation	IMP PMID:10080719 Genetic and physical characterization of a region of Arabido...	MODIFY	Summary: CLV1 signaling affects the balance between meristem cell proliferation and differentiation, but this broad term and the mapping-focused reference do not capture the specific CLV1 process. A meristem-specific regulation term is already present and better represents the evidence. Reason: "Cell differentiation" is too broad for CLV1. The functional evidence is specifically about meristem stem-cell homeostasis and meristem structural organization. Proposed replacements: regulation of meristem structural organization Supporting Evidence: PMID:9160749 Normally, proliferation and differentiation are balanced, so that the structure and size of the shoot meristem is maintained. PMID:20626648 CLAVATA1 (CLV1), CLV2, CLV3, CORYNE (CRN), BAM1 and BAM2 are key regulators that function at the shoot apical meristem (SAM) of plants to promote differentiation by limiting the size of the organizing center that maintains stem cell identity in neighboring cells.
GO:0036289 peptidyl-serine autophosphorylation	IDA PMID:9701578 Control of meristem development by CLAVATA1 receptor kinase ...	ACCEPT	Summary: CLV1 autophosphorylation is experimentally demonstrated and is central to its receptor kinase mechanism and interaction with KAPP. Reason: Autophosphorylation is a direct biochemical property of CLV1 and helps explain recruitment of phospho-binding regulators. Supporting Evidence: PMID:9701578 KAPP binds directly to autophosphorylated CLV1 in vitro and co-immunoprecipitates with CLV1 in plant extracts derived from meristematic tissue. PMID:9294234 CLV1 has kinase activity: it phosphorylates both itself and KAPP.
GO:0004672 protein kinase activity	IEA GO_REF:0000002	MODIFY	Summary: Protein kinase activity is correct but too general for CLV1, which is experimentally and domain-supported as a Ser/Thr receptor-like kinase. Reason: Replace the generic kinase term with the more informative Ser/Thr protein kinase term already supported by direct assays and EC mapping. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:9294234 CLV1 has kinase activity: it phosphorylates both itself and KAPP. file:interpro/panther/PTHR48056/PTHR48056-metadata.yaml Members of this family function as receptors that perceive various extracellular signals, such as peptide hormones, brassinosteroids, and pathogen-associated molecular patterns, to regulate cellular processes.
GO:0004674 protein serine/threonine kinase activity	IEA GO_REF:0000003	ACCEPT	Summary: EC mapping to protein Ser/Thr kinase activity is consistent with CLV1 sequence features, direct kinase/autophosphorylation assays, and more recent evidence for CLV1 phosphorylation of downstream RLCKs. Reason: Ser/Thr protein kinase activity is a core molecular function of CLV1. Supporting Evidence: PMID:9294234 CLV1 has kinase activity: it phosphorylates both itself and KAPP. PMID:34935965 PBL34/35/36 interacted with CLV1, BAM1/3, and CIKs, and were phosphorylated by CLV1 and BAM1.
GO:0004674 protein serine/threonine kinase activity	IDA PMID:34651321 A CLE-BAM-CIK signalling module controls root protophloem di...	ACCEPT	Summary: The CLE25/26/45-BAM/CLV1-CIK work supports a CLV1-containing receptor module required for CIK phosphorylation during root protophloem signaling. Together with direct kinase assays from other CLV1 studies, this supports Ser/Thr kinase activity. Reason: The annotation is biologically correct, although PMID:34651321 supports the receptor-module phosphorylation event more directly than isolated CLV1 catalytic activity. Supporting Evidence: PMID:34651321 CLE25/26/45 enhanced the phosphorylation levels of CIKs, which were greatly impaired in clv1 bam1 3 mutant. PMID:34935965 Further biochemical assays revealed that PBL34/35/36 interacted with CLV1, BAM1/3, and CIKs, and were phosphorylated by CLV1 and BAM1.
GO:0004674 protein serine/threonine kinase activity	IDA PMID:9701578 Control of meristem development by CLAVATA1 receptor kinase ...	ACCEPT	Summary: CLV1 kinase activity is directly supported by phosphorylation of itself and KAPP, and by KAPP binding to autophosphorylated CLV1. Reason: Ser/Thr kinase activity is the catalytic core of the CLV1 receptor. Supporting Evidence: PMID:9701578 KAPP binds directly to autophosphorylated CLV1 in vitro and co-immunoprecipitates with CLV1 in plant extracts derived from meristematic tissue. PMID:9294234 CLV1 has kinase activity: it phosphorylates both itself and KAPP.
GO:0005515 protein binding	IPI PMID:10393905 Kinase interaction domain of kinase-associated protein phosp...	MODIFY	Summary: This KAPP/CLV1 interaction is real but "protein binding" is too generic. The biology is binding of CLV1 to the protein phosphatase KAPP through a phosphorylation-dependent kinase interaction domain. Reason: Replace generic protein binding with protein phosphatase binding. Proposed replacements: protein phosphatase binding Supporting Evidence: PMID:10393905 Kinase-associated protein phosphatase interacts specifically with plant receptor-like protein kinases. PMID:10393905 the observed weaker binding signal of the CLV1 to the KI domain in comparison to the interaction of KIK1 and the KI domain is likely the result of less phosphorylation on KI domain-binding sites of CLV1 than KIK1.
GO:0005515 protein binding	IPI PMID:19452453 Proteomic profiling of tandem affinity purified 14-3-3 prote...	MODIFY	Summary: The reference is a proteomic survey of TAP-purified 14-3-3 omega complexes. This may indicate a CLV1 14-3-3 association, but it is high-throughput and not a core CLV1 function. Reason: If retained, this should use the specific 14-3-3 protein binding term rather than generic protein binding, and should not be interpreted as a core CLV1 activity without focused validation. Proposed replacements: 14-3-3 protein binding Supporting Evidence: PMID:19452453 Purified complexes were analyzed by tandem MS. PMID:19452453 The identification here of 121 putative clients provides support for in vivo 14-3-3 interactions with a diverse array of proteins
GO:0005515 protein binding	IPI PMID:19525968 A glycopeptide regulating stem cell fate in Arabidopsis thal...	MODIFY	Summary: The evidence supports high-affinity binding of mature arabinosylated CLV3 glycopeptide to CLV1. Generic protein binding obscures the ligand-receptor relationship. Reason: Replace generic protein binding with peptide hormone binding for CLV3 and CLE2 peptide ligands. Proposed replacements: peptide hormone binding Supporting Evidence: PMID:19525968 Post-translational arabinosylation of CLV3 is critical for its biological activity and high-affinity binding to its receptor CLV1.
GO:0005515 protein binding	IPI PMID:19843317 Analysis of interactions among the CLAVATA3 receptors reveal...	MODIFY	Summary: The study supports weak interaction of CLV1 with CRN and interaction with CLV2-CRN heterodimers. Generic protein binding should be replaced by a receptor kinase/co-receptor binding term. Reason: The interaction concerns receptor-like kinase components of the CLV signaling pathway, not nonspecific protein binding. Proposed replacements: receptor serine/threonine kinase binding Supporting Evidence: PMID:19843317 Additional LCI assays showed that CLV1 did not interact with CLV2, but can interact weakly with CRN. PMID:19843317 We also found that CLV1 can interact with CLV2-CRN heterodimers, implying that these three proteins may form a complex.
GO:0005515 protein binding	IPI PMID:20626648 CLAVATA2 forms a distinct CLE-binding receptor complex regul...	MODIFY	Summary: PMID:20626648 supports several CLV1 interaction classes: CLV1 homomerization, CLV1-BAM receptor complexes, weaker CLV1-CLV2/CRN interactions, and CLV3/CLE peptide binding. The existing generic protein binding rows should be split into specific binding terms. Reason: Replace generic protein binding with specific peptide hormone binding for CLE ligands and receptor Ser/Thr kinase binding for CLV1/BAM receptor-complex partners. Proposed replacements: peptide hormone binding receptor serine/threonine kinase binding Supporting Evidence: PMID:20626648 CLV2, CLV1 and the CLV1 homologs BAM1 and BAM2 all bind to the CLV3-derived CLE peptide with similar kinetics PMID:20626648 We first tested interactions among the related receptor-kinases CLV1, BAM1 and BAM2. We observed robust co-IP between CLV1-CLV1, CLV1-BAM1, CLV1-BAM2, BAM1-BAM1, and BAM1-BAM2
GO:0005515 protein binding	IPI PMID:29320478 An extracellular network of Arabidopsis leucine-rich repeat ...	UNDECIDED	Summary: The paper is a high-throughput extracellular-domain interaction network for Arabidopsis LRR receptor kinases, but the cached text does not expose the CLV1-specific IntAct partners for this GOA row. The general study is relevant, but the specific CLV1 binding claim cannot be checked from the available cached evidence. Reason: Use UNDECIDED because the CLV1-specific interaction evidence is in supplementary/network data not available in the cached text reviewed here. Supporting Evidence: PMID:29320478 we investigated 40,000 potential ECD interactions using a sensitized high-throughput interaction assay, and produced an LRR-based cell surface interaction network (CSILRR) that consists of 567 interactions.
GO:0005515 protein binding	IPI PMID:29581511 A group of receptor kinases are essential for CLAVATA signal...	MODIFY	Summary: CLV1 physically and functionally associates with CIK co-receptor kinases during CLV3 signal transduction. Generic protein binding is not the best term. Reason: Replace generic protein binding with receptor Ser/Thr kinase binding for CIK co-receptor association. Proposed replacements: receptor serine/threonine kinase binding Supporting Evidence: PMID:29581511 Genetic analyses and biochemical assays demonstrated that CIKs function as co-receptors of CLV1, CLV2/CRN and RPK2 to mediate CLV3 signalling through phosphorylation.
GO:0005515 protein binding	IPI PMID:33909893 Receptor-like cytoplasmic kinase MAZZA mediates developmenta...	MODIFY	Summary: CLV1-family receptors interact in vivo with MAZ and related Pti1-like receptor-like cytoplasmic kinases during stomatal and root development. This is a specific signaling-partner interaction, not generic protein binding. Reason: Replace generic protein binding with kinase binding, while treating this as context-specific/non-core relative to the canonical CLV3 meristem receptor role. Proposed replacements: kinase binding Supporting Evidence: PMID:33909893 the membrane-associated receptor-like cytoplasmic kinase (RLCK) MAZZA (MAZ) and additional members of the Pti1-like protein family interact in vivo with CLV1f receptors. PMID:33909893 We identified a role for a CLV1-MAZ signaling module during stomatal and root development
GO:0005515 protein binding	IPI PMID:34935965 Receptor-like cytoplasmic kinases PBL34/35/36 are required f...	MODIFY	Summary: CLV1 interacts with the receptor-like cytoplasmic kinases PBL34/35/36 and phosphorylates them. Generic protein binding should be replaced by kinase binding. Reason: The evidence concerns CLV1 binding of downstream cytoplasmic kinases in CLE peptide signaling. Proposed replacements: kinase binding Supporting Evidence: PMID:34935965 Further biochemical assays revealed that PBL34/35/36 interacted with CLV1, BAM1/3, and CIKs, and were phosphorylated by CLV1 and BAM1.
GO:0005515 protein binding	IPI PMID:9294234 A possible role for kinase-associated protein phosphatase in...	MODIFY	Summary: CLV1 binds the protein phosphatase KAPP, which dephosphorylates CLV1 and negatively regulates the pathway. Generic protein binding is too broad. Reason: Replace generic protein binding with protein phosphatase binding. Proposed replacements: protein phosphatase binding Supporting Evidence: PMID:9294234 KAPP binds and dephosphorylates CLV1. PMID:9294234 We present a model where KAPP functions as a negative regulator of the CLAVATA1 signal transduction pathway.
GO:0005515 protein binding	IPI PMID:9701578 Control of meristem development by CLAVATA1 receptor kinase ...	MODIFY	Summary: CLV1 binds KAPP in vitro and in meristematic tissue extracts. This should be represented as protein phosphatase binding, not generic protein binding. Reason: Replace generic protein binding with protein phosphatase binding. Proposed replacements: protein phosphatase binding Supporting Evidence: PMID:9701578 KAPP binds directly to autophosphorylated CLV1 in vitro and co-immunoprecipitates with CLV1 in plant extracts derived from meristematic tissue.
GO:0005524 ATP binding	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: ATP binding is expected for the conserved cytoplasmic protein kinase domain and is required for CLV1 phosphorylation reactions. It is correct but generic and should not be treated as a distinct core function apart from Ser/Thr kinase activity. Reason: Keep as a mechanistic cofactor-binding annotation for the kinase domain, but the core function is Ser/Thr receptor kinase signaling. Supporting Evidence: file:ARATH/CLV1/CLV1-uniprot.txt BINDING 698..706 file:ARATH/CLV1/CLV1-uniprot.txt /ligand="ATP"
GO:0033612 receptor serine/threonine kinase binding	IPI PMID:20626648 CLAVATA2 forms a distinct CLE-binding receptor complex regul...	ACCEPT	Summary: CLV1 forms receptor-kinase complexes with CLV1/BAM family members and weaker interactions with CLV2/CRN components. The term is specific and well supported for CLV1-BAM receptor complex formation. Reason: This specific binding term is appropriate for CLV1 receptor-complex organization. Supporting Evidence: PMID:20626648 We first tested interactions among the related receptor-kinases CLV1, BAM1 and BAM2. We observed robust co-IP between CLV1-CLV1, CLV1-BAM1, CLV1-BAM2, BAM1-BAM1, and BAM1-BAM2 PMID:20626648 we tested co-IP between CLV1-GFP and CLV1-FLAG in Arabidopsis meristem tissue.
GO:0106310 protein serine kinase activity	ISS GO_REF:0000024	ACCEPT	Summary: Protein serine kinase activity is consistent with CLV1's conserved Ser/Thr kinase domain and direct autophosphorylation evidence. It is narrower than the better-established Ser/Thr kinase term but not contradicted by the literature. Reason: CLV1 is a Ser/Thr protein kinase, and serine autophosphorylation is directly annotated from experimental evidence. Supporting Evidence: PMID:9701578 KAPP binds directly to autophosphorylated CLV1 in vitro and co-immunoprecipitates with CLV1 in plant extracts derived from meristematic tissue.
GO:0106310 protein serine kinase activity	IEA GO_REF:0000116	ACCEPT	Summary: Rhea-based inference to protein serine kinase activity is compatible with the CLV1 kinase domain and experimental autophosphorylation data. Reason: This is correct as part of CLV1's Ser/Thr kinase molecular activity, though GO:0004674 gives the broader experimentally supported activity. Supporting Evidence: PMID:9294234 CLV1 has kinase activity: it phosphorylates both itself and KAPP.
GO:0032502 developmental process	IEA GO_REF:0000117	MODIFY	Summary: CLV1 is clearly involved in plant development, but "developmental process" is much too broad and hides the specific role in meristem and CLE peptide signaling. Reason: Replace the broad ARBA developmental annotation with the existing meristem-specific process. Proposed replacements: regulation of meristem structural organization Supporting Evidence: PMID:9160749 CLV1 expression in the inflorescence is specifically associated with meristematic activity.
GO:0035556 intracellular signal transduction	IDA PMID:34651321 A CLE-BAM-CIK signalling module controls root protophloem di...	ACCEPT	Summary: CLE25/26/45 signaling depends on CLV1/BAM receptor modules and CIK phosphorylation; related work places PBL34/35/36 downstream of CLV1 for intracellular signal transmission. The term is broad but appropriate as a signaling-process annotation. Reason: CLV1 is a membrane receptor kinase whose intracellular domain transduces extracellular CLE peptide perception into phosphorylation-dependent cytoplasmic signaling. Supporting Evidence: PMID:34651321 Our work clarifies that the CLE25/26/45-BAM1/3-CIK2/3/4/5/6 signalling module genetically acts downstream of BRX and OPS to suppress protophloem differentiation. PMID:34935965 All these results suggest that PBL34/35/36 act downstream of CLV1 and BAM1/3 to mediate the CLV3 and CLE25/26/45 signals in maintaining SAM and RAM homeostasis, respectively.
GO:0050793 regulation of developmental process	IEA GO_REF:0000117	MODIFY	Summary: The broad ARBA term is directionally correct but over-general for CLV1. The literature supports specific developmental signaling processes, especially meristem structural organization and stomatal/root context regulation. Reason: Use the more precise meristem process for the core developmental role of CLV1. Proposed replacements: regulation of meristem structural organization Supporting Evidence: PMID:29581511 CIKs function as co-receptors of CLV1, CLV2/CRN and RPK2 to mediate CLV3 signalling through phosphorylation.
GO:2000037 regulation of stomatal complex patterning	IMP PMID:33909893 Receptor-like cytoplasmic kinase MAZZA mediates developmenta...	KEEP AS NON CORE	Summary: CLV1-family receptors and MAZ/Pti1-like cytoplasmic kinases participate in stomatal and root development. The specific stomatal patterning role is supported but context-specific and likely partly redundant. Reason: Keep as a valid non-core developmental context for CLV1-family signaling; the core CLV1 function remains CLE peptide receptor kinase signaling in meristem homeostasis. Supporting Evidence: PMID:33909893 We identified a role for a CLV1-MAZ signaling module during stomatal and root development PMID:33909893 MAZ, and related RLCKs, mediate CLV1f signaling in a variety of developmental contexts
GO:0005886 plasma membrane	IEA GO_REF:0000044	ACCEPT	Summary: Plasma membrane localization is strongly supported by CLV1 topology, imaging, and functional receptor-complex studies. Reason: CLV1 functions as a cell-surface receptor kinase at the plasma membrane. Supporting Evidence: PMID:21051944 All tested proteins measurably accumulate at the plasma membrane. PMID:21051944 CLV1 primarily co-localizes with a plasma membrane marker
GO:0005886 plasma membrane	ISM GO_REF:0000122	ACCEPT	Summary: The computational subcellular annotation is correct and is supported by experimental plasma membrane localization. Reason: CLV1 is a single-pass receptor kinase that acts at the plasma membrane. Supporting Evidence: PMID:23394827 Both CLV1 and ACR4 overlap in their expression domains in the distal root meristem and localize to the plasma membrane (PM) and plasmodesmata (PDs)
GO:0005886 plasma membrane	EXP PMID:19933383 Stem cell signaling in Arabidopsis requires CRN to localize ...	ACCEPT	Summary: CLV1 homomers localize to the plasma membrane independently of CLV2 and CRN, supporting a plasma membrane receptor-complex role. Reason: The cellular location matches CLV1's receptor function. Supporting Evidence: PMID:19933383 CLV1 forms homomers independently of CLV2 and CRN at the PM. PMID:19933383 a CLV1 homodimer that localize to the PM
GO:0005886 plasma membrane	IDA PMID:21051944 Membrane distributions of two ligand-binding receptor comple...	ACCEPT	Summary: Direct membrane partitioning and marker co-localization support CLV1 accumulation at the plasma membrane. Reason: Plasma membrane localization is the site of extracellular CLE peptide perception by CLV1. Supporting Evidence: PMID:21051944 All tested proteins measurably accumulate at the plasma membrane. PMID:21051944 CLV1 primarily co-localizes with a plasma membrane marker
GO:0005886 plasma membrane	IDA PMID:29581511 A group of receptor kinases are essential for CLAVATA signal...	ACCEPT	Summary: CLV1 functions with CIK co-receptors in CLV3 signaling; this receptor/co-receptor module is consistent with plasma membrane localization and is supported by the broader experimental localization literature. Reason: Correct cellular component for the CLV1 receptor signaling complex. Supporting Evidence: PMID:29581511 CIKs function as co-receptors of CLV1, CLV2/CRN and RPK2 to mediate CLV3 signalling through phosphorylation. PMID:21051944 CLV1 primarily co-localizes with a plasma membrane marker
GO:0005886 plasma membrane	EXP PMID:33909893 Receptor-like cytoplasmic kinase MAZZA mediates developmenta...	ACCEPT	Summary: CLV1-family CLE receptor complexes form at the plasma membrane, and MAZ localizes to the plasma membrane to interact with CLV1-family receptors. Reason: This supports CLV1-family signaling at the plasma membrane in additional developmental contexts. Supporting Evidence: PMID:33909893 CLE peptide signaling, which is required for meristem size control, vascular development, and pathogen responses, involves the formation of receptor complexes at the plasma membrane. PMID:33909893 MAZ, which is widely expressed throughout the plant, localizes to the plasma membrane via post-translational palmitoylation
GO:0016020 membrane	ISS PMID:9160749 The CLAVATA1 gene encodes a putative receptor kinase that co...	MODIFY	Summary: CLV1 is a membrane receptor kinase, but "membrane" is too general given strong experimental evidence for plasma membrane localization. Reason: Replace with the more precise and experimentally supported plasma membrane term. Proposed replacements: plasma membrane Supporting Evidence: PMID:9160749 The extracellular domain is composed of 21 tandem leucine-rich repeats that resemble leucine-rich repeats found in animal hormone receptors. PMID:21051944 CLV1 primarily co-localizes with a plasma membrane marker
GO:0000325 plant-type vacuole	IDA PMID:21333538 Plant stem cell signaling involves ligand-dependent traffick...	KEEP AS NON CORE	Summary: CLV1 is trafficked to the lytic vacuole after CLV3 ligand perception. This is a regulated trafficking/degradation location rather than the primary site of receptor signaling. Reason: Keep as a valid ligand-dependent trafficking annotation but not as the core active location; core signaling occurs at the plasma membrane. Supporting Evidence: PMID:21333538 plasma membrane-localized CLV1 is reduced in concentration by CLV3, which causes trafficking of CLV1 to lytic vacuoles. PMID:21333538 CLV3 is both necessary and sufficient to drive depletion of CLV1 from the PM in apical meristems, followed by trafficking to the lytic vacuole in a post-transcriptional manner.
GO:0009506 plasmodesma	IDA PMID:23394827 Moderation of Arabidopsis root stemness by CLAVATA1 and ARAB...	KEEP AS NON CORE	Summary: CLV1 and ACR4 localize to plasma membrane and plasmodesmata in distal root meristem cells and form homo- and heteromeric complexes. This is supported but is context-specific for root stemness signaling. Reason: Keep as a non-core localization relevant to root meristem signaling; plasma membrane receptor kinase activity remains the main cellular role. Supporting Evidence: PMID:23394827 Both CLV1 and ACR4 overlap in their expression domains in the distal root meristem and localize to the plasma membrane (PM) and plasmodesmata (PDs), where ACR4 preferentially accumulates. PMID:23394827 CLV1 and ACR4 can form homo- and heteromeric complexes that differ in their composition depending on their subcellular localization.

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