SHOOT MERISTEMLESS (STM; At1g62360) encodes a class I KNOX/TALE homeobox transcription factor that is central to Arabidopsis shoot apical meristem initiation and maintenance. STM acts primarily as a sequence-specific DNA-binding transcription factor in the nucleus, where its activity depends on KNOX/TALE homeodomain architecture and heterodimerization with BELL/BLH homeodomain partners. It suppresses differentiation and promotes cell division in the meristem dome, contributes to CLV3/stem-cell homeostasis with WUSCHEL, and activates cytokinin biosynthesis as part of the meristem maintenance program. STM is also a mobile protein whose localization is regulated by BELL/BLH partners, MBP2C, and FTIP3/FTIP4; it can traffic through plasmodesmata, with cytoplasm, endosome, plasma membrane, and microtubule- associated puncta representing trafficking/regulatory states rather than the primary site of transcriptional activity. Later reproductive roles in floral fate and carpel initiation are well supported, but are best treated as developmental contexts downstream of the core STM function in maintaining meristematic identity.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009691 cytokinin biosynthetic process | TAS PMID:16139212 Arabidopsis KNOXI proteins activate cytokinin biosynthesis. | ACCEPT | Summary: STM is not a cytokinin biosynthetic enzyme, but the annotation uses a BP qualifier and is supported by evidence that inducible STM rapidly increases AtIPT7 expression and cytokinin levels, and that cytokinin can partially rescue stm defects. Reason: Activation of cytokinin biosynthesis is a direct and biologically central part of the KNOX/STM meristem maintenance program, so retaining this BP annotation is appropriate. Supporting Evidence: PMID:16139212 activation of cytokinin biosynthesis mediates KNOXI function in meristem maintenance PMID:16139212 rapid and dramatic increase in cytokinin levels following activation of the KNOXI protein SHOOT MERISTEMLESS (STM) |
| GO:0009934 regulation of meristem structural organization | IMP PMID:12070094 The WUSCHEL and SHOOTMERISTEMLESS genes fulfil complementary... | ACCEPT | Summary: STM suppresses differentiation across the meristem dome and promotes cell division independently of WUS, matching a role in regulating meristem organization. Reason: This is a core biological process for STM. The publication directly separates STM's function from WUS and places STM in maintenance of the undifferentiated meristem structure. Supporting Evidence: PMID:12070094 STM suppresses differentiation independently of WUS and is required and sufficient to promote cell division PMID:12070094 STM is required to suppress differentiation throughout the meristem dome |
| GO:0010582 floral meristem determinacy | IGI PMID:29743198 The KNOXI Transcription Factor SHOOT MERISTEMLESS Regulates ... | KEEP AS NON CORE | Summary: STM contributes to floral fate in sensitized reproductive backgrounds, including AP1 and UFO genetic contexts. This is a real later developmental role, but it is not the primary evolved molecular function of STM. Reason: The term is supported for reproductive development, but STM's core role is maintenance of meristematic identity by transcriptional regulation. Floral meristem determinacy should be retained as a context-specific developmental function rather than promoted as the core function. Supporting Evidence: PMID:29743198 Here, we uncover a role for STM in the specification of flower meristem identity PMID:29743198 stm-2 enhanced the ufo-2 floral fate phenotype |
| GO:0019827 stem cell population maintenance | TAS PMID:12068101 Regulation of CLV3 expression by two homeobox genes in Arabi... | ACCEPT | Summary: STM contributes to meristem stem-cell homeostasis, including later CLV3 expression together with WUS. This is consistent with STM's broader role in suppressing differentiation in meristem cells. Reason: Stem cell population maintenance is a core STM process-level annotation, supported by CLV3 regulatory evidence and by independent meristem maintenance studies. Supporting Evidence: PMID:12068101 At later developmental stages, WUS promotes the level of CLV3 expression, together with STM PMID:12068101 Homeostasis of the stem cell population may be achieved through feedback regulation |
| GO:0048440 carpel development | IMP PMID:17461793 The KNOX gene SHOOT MERISTEMLESS is required for the develop... | KEEP AS NON CORE | Summary: Loss and ectopic-expression experiments support a role for STM in carpel initiation and reproductive meristematic tissues. This is a true developmental role but is downstream of the general KNOX meristem program. Reason: Retain the annotation because the phenotype is specific and experimentally supported, but mark it non-core because STM's core function is transcriptional maintenance of meristem identity rather than carpel-specific identity specification. Supporting Evidence: PMID:17461793 complete loss of carpel development PMID:17461793 indicate a specific requirement for STM in carpel initiation |
| GO:0005737 cytoplasm | IPI PMID:29742441 FTIP-Dependent STM Trafficking Regulates Shoot Meristem Deve... | KEEP AS NON CORE | Summary: STM can be found outside the nucleus during FTIP-dependent trafficking. The cytoplasmic annotation is compatible with the trafficking model but is not the main site of STM transcription factor activity. Reason: The annotation should be retained as a trafficking/localization state, but it should not be treated as a core active location for STM's DNA-binding transcription factor activity. Supporting Evidence: PMID:29742441 This facilitates STM recycling to the nucleus file:ARATH/STM/STM-uniprot.txt Cytoplasm {ECO:0000269|PubMed:17965274} |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: STM is a TALE/KNOX homeodomain protein and the UniProt record states that it probably binds the 5'-TGAC-3' DNA sequence. Phylogenetic inference from the TALE homeobox family is consistent with sequence-specific regulatory DNA binding. Reason: This is one of the most informative MF annotations for STM and directly supports the core transcription-factor function. Supporting Evidence: file:ARATH/STM/STM-uniprot.txt Probably binds to the DNA sequence 5'-TGAC-3' file:interpro/panther/PTHR11850/PTHR11850-metadata.yaml The TALE homeobox family is characterized by a conserved DNA-binding homeodomain |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IEA GO_REF:0000002 | ACCEPT | Summary: STM is a KNOX/TALE homeodomain transcription factor that regulates meristem gene expression. Although this row is electronically inferred, the term accurately captures the core molecular activity better than the older broader GO:0003700 term. Reason: STM's best-supported core MF is RNA polymerase II-specific DNA-binding transcription factor activity in the nucleus. Supporting Evidence: PMID:12070094 ectopic WUS and STM activities induce the expression of different downstream target genes file:ARATH/STM/STM-uniprot.txt STM encodes a Knotted-like homeodomain-containing protein and is likely to act as a transcriptional regulator file:ARATH/STM/STM-deep-research-falcon.md STM (At1g62360; UniProt Q38874) encodes a mobile TALE/KNOX homeodomain transcription factor |
| GO:0003676 nucleic acid binding | IEA GO_REF:0000117 | MODIFY | Summary: This ARBA-derived annotation is too broad. STM's supported nucleic-acid binding role is sequence-specific regulatory DNA binding as a TALE/KNOX transcription factor; the RNA-binding claim is not well supported for Arabidopsis STM by the accessible evidence. Reason: Replace the generic parent term with specific regulatory DNA-binding and RNA polymerase II transcription factor terms. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: file:ARATH/STM/STM-uniprot.txt Probably binds to the DNA sequence 5'-TGAC-3' |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | MODIFY | Summary: DNA binding is correct but underspecified for a homeodomain transcription factor. STM should be represented by regulatory-region sequence-specific DNA binding. Reason: The existing term is true but less informative than GO:0000978 for STM's core DNA-binding activity. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: file:ARATH/STM/STM-uniprot.txt Probably binds to the DNA sequence 5'-TGAC-3' |
| GO:0003700 DNA-binding transcription factor activity | IBA GO_REF:0000033 | MODIFY | Summary: The phylogenetic annotation correctly identifies STM as a DNA-binding transcription factor, but GO:0000981 is the more specific current term for RNA polymerase II-specific DNA-binding transcription factor activity. Reason: Retain the substance of the annotation but replace the broad parent term with the more precise GO term already present for STM. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000219731 · homeodomain transcription factor family node SUPPORTS TRANSFER Broad DNA-binding transcription factor IBD seeded by many metazoan and fungal homeodomain TFs; the transfer is sound and the Pol II-specific child term is the appropriate refinement for STM. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: file:interpro/panther/PTHR11850/PTHR11850-metadata.yaml Members of this family function as transcription factors |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | MODIFY | Summary: This older comparative-genomics reference supports classification of Arabidopsis homeodomain proteins as transcription factors, but the term is now less specific than GO:0000981. Reason: The annotation is directionally correct but should be modernized to the more precise RNA polymerase II-specific DNA-binding transcription factor activity term. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:11118137 The genome-wide comparison reveals the evolutionary generation of diversity in the regulation of transcription file:ARATH/STM/STM-uniprot.txt STM encodes a Knotted-like homeodomain-containing protein and is likely to act as a transcriptional regulator |
| GO:0003723 RNA binding | IDA PMID:17965274 MPB2C, a microtubule-associated protein, regulates non-cell-... | REMOVE | Summary: The accessible local text for PMID:17965274 supports MPB2C as an RNA and homeodomain-motif binding protein and supports MPB2C binding to KN1/STM. It does not provide direct evidence that Arabidopsis STM itself binds RNA. UniProt lists STM RNA binding only by similarity. Reason: The cached full text of PMID:17965274 attributes the RNA-binding activity to MPB2C, not STM (the paper states that MPB2C "is an RNA and HD motif binding protein"); STM appears in the paper only as an MPB2C interaction partner, and no STM RNA-binding assay is reported. The IDA RNA-binding annotation therefore mis-assigns the partner protein's activity to STM and should be removed. Supporting Evidence: PMID:17965274 Here, we show that MPB2C is an RNA and HD motif binding protein file:ARATH/STM/STM-uniprot.txt Binds to RNA (By similarity) |
| GO:0005515 protein binding | IPI PMID:11701881 The Arabidopsis BELL1 and KNOX TALE homeodomain proteins int... | MODIFY | Summary: The BEL1/KNOX interaction is real and functionally relevant, but the term protein binding is too generic for STM. The evidence supports heterodimerization of TALE homeodomain proteins. Reason: Replace generic protein binding with protein heterodimerization activity, which better captures the KNOX-BELL interaction mechanism. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:11701881 BEL1 and KNAT proteins can activate transcription only as a heterodimeric complex PMID:11701881 suggest a role for the BEL1-STM complex in maintaining the indeterminacy of the inflorescence meristem |
| GO:0005515 protein binding | IPI PMID:12897247 The interaction of two homeobox genes, BREVIPEDICELLUS and P... | MODIFY | Summary: This row records a generic BELL/KNOX interaction. The original abstract emphasizes BP-PNY more than STM, but broader STM-BELL interaction evidence supports the same heterodimerization mechanism. Reason: The annotation should not remain as generic protein binding; KNOX-BELL heterodimerization is the informative molecular function. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:12897247 KNOX proteins interact with BEL1-like (BELL) homeodomain proteins PMID:16513846 STM is targeted into the nuclear compartment through heterodimerization with BLH partner proteins |
| GO:0005515 protein binding | IPI PMID:15019989 VAAMANA--a BEL1-like homeodomain protein, interacts with KNO... | MODIFY | Summary: VAAMANA/PNY interaction with STM is supported, but generic protein binding obscures the TALE homeodomain heterodimerization mechanism. Reason: Replace with protein heterodimerization activity, a more informative term for the STM-BELL interaction. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:15019989 VAN interacts specifically with the class I KNOX proteins SHOOTMERISTEMLESS (STM), BREVIPEDICELLUS (BP), and KNAT6 (K6) |
| GO:0005515 protein binding | IPI PMID:15781858 A central role of Arabidopsis thaliana ovate family proteins... | MODIFY | Summary: The study supports a network of TALE homeodomain interactions, including BELL/KNOX heterodimerization, but protein binding is an unhelpful generic label for STM. Reason: The more specific term protein heterodimerization activity better captures the TALE partner interactions. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:15781858 Every member of the KNOX family has at least one interaction partner amongst the BELL proteins PMID:15781858 supporting the notion that BELL/KNOX heterodimerization plays a general role in TALE protein function |
| GO:0005515 protein binding | IPI PMID:16513846 Nuclear import of the transcription factor SHOOT MERISTEMLES... | MODIFY | Summary: This interaction evidence is directly relevant to STM function because BLH partners mediate STM nuclear import, but the GO term should be more specific than protein binding. Reason: STM-BLH heterodimerization is the functional interaction; generic protein binding should be replaced with GO:0046982. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:16513846 STM is targeted into the nuclear compartment through heterodimerization with BLH partner proteins |
| GO:0005515 protein binding | IPI PMID:17785527 Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit ... | MODIFY | Summary: The cached abstract for this paper does not discuss STM, but the GOA row is an IntAct-derived interaction with ATH1 and the STM-ATH1 interaction is directly supported by PMID:16513846. The term still needs replacement by a more specific heterodimerization term. Reason: Do not retain generic protein binding as a core MF; curate the supported STM-ATH1 interaction as TALE protein heterodimerization. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:16513846 STM is targeted into the nuclear compartment through heterodimerization with BLH partner proteins file:ARATH/STM/STM-uniprot.txt Q38874; P48731: ATH1; NbExp=9 |
| GO:0005515 protein binding | IPI PMID:17873098 The Arabidopsis BEL1-LIKE HOMEODOMAIN proteins SAW1 and SAW2... | MODIFY | Summary: This paper supports KNOX-BLH functional interaction in shoot development. The current term protein binding is too broad for the STM-BELLRINGER/BLH interaction class. Reason: Replace the generic term with protein heterodimerization activity and keep the biological interpretation tied to KNOX-BLH complexes. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:17873098 KNOX proteins interact with specific members of BLH proteins in Arabidopsis PMID:17873098 BLH proteins BLR and PNF and Class 1 KNOX TALE homeodomain proteins BP and STM interact to positively regulate growth |
| GO:0005515 protein binding | IPI PMID:17965274 MPB2C, a microtubule-associated protein, regulates non-cell-... | MODIFY | Summary: STM binds MBP2C, a microtubule-associated protein that regulates KNOX cell-to-cell trafficking. This is real but not well represented by generic protein binding. Reason: The specific function supported by the publication is binding to a cytoskeletal/microtubule-associated regulator, so cytoskeletal protein binding is more informative than protein binding. Proposed replacements: cytoskeletal protein binding Supporting Evidence: PMID:17965274 At MPB2C, are KN1/STM binding factors PMID:17965274 MPB2C is an RNA and HD motif binding protein that functions as a component in the regulation of KN1 trafficking |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | REMOVE | Summary: CrY2H-seq is a valuable high-throughput interaction resource, but this generic protein binding row adds no specific STM functional mechanism beyond better targeted KNOX-BELL studies. Reason: High-throughput PPI evidence without STM-specific functional validation is not sufficient to keep a generic protein binding annotation in the curated core/non-core set. Supporting Evidence: PMID:28650476 ten independent screens testing a total of 36 million binary interaction combinations PMID:28650476 uncovering a network of 8,577 interactions among 1,453 transcription factors |
| GO:0005515 protein binding | IPI PMID:29742441 FTIP-Dependent STM Trafficking Regulates Shoot Meristem Deve... | MARK AS OVER ANNOTATED | Summary: STM interaction with FTIP3/FTIP4 is functionally important for trafficking and nuclear recycling, but protein binding is too generic and is not the core STM MF. Reason: Retain the biological insight as trafficking regulation, but avoid promoting generic protein binding. The existing localization and transport annotations capture the consequence more informatively. Supporting Evidence: PMID:29742441 FTIP3/4 prevent intracellular trafficking of a key regulator, SHOOTMERISTEMLESS (STM), to the plasma membrane file:ARATH/STM/STM-uniprot.txt Interacts with FTIP3 and FTIP4 (PubMed:29742441) |
| GO:0005515 protein binding | IPI PMID:36088536 The protein-protein interaction landscape of transcription f... | REMOVE | Summary: This is a process-specific high-throughput gynoecium TF interaction map. The cached abstract does not provide STM-specific mechanistic validation, and the generic term is uninformative. Reason: Remove as a generic protein binding annotation based on broad PPI mapping. More specific and better validated STM-BELL interaction annotations are already represented above. Supporting Evidence: PMID:36088536 mapping binary interactions between well-characterized TFs PMID:36088536 detected more than 250 protein-protein interactions |
| GO:0042803 protein homodimerization activity | IDA PMID:17965274 MPB2C, a microtubule-associated protein, regulates non-cell-... | KEEP AS NON CORE | Summary: UniProt records STM homodimerization with PMID:17965274 support. This is a plausible non-core molecular property of STM, distinct from its main sequence-specific transcription factor activity. Reason: Homodimerization may contribute to STM behavior, but core function is best represented by transcription factor activity and KNOX-BELL heterodimer regulation. Supporting Evidence: file:ARATH/STM/STM-uniprot.txt Forms homodimers (PubMed:17965274) |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: STM regulates transcription, but the term is broader than needed and does not specify RNA polymerase II transcription. Reason: Replace this broad BP term with GO:0006357, which is already present and better aligned with STM's RNA polymerase II transcription factor activity. Proposed replacements: regulation of transcription by RNA polymerase II Supporting Evidence: PMID:12070094 ectopic WUS and STM activities induce the expression of different downstream target genes |
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: This BP annotation is appropriate for STM as a homeodomain transcription factor acting on regulatory targets in meristem cells. Reason: Regulation of RNA polymerase II transcription is central to STM's molecular mechanism and is supported by TALE family context and STM developmental genetics. Supporting Evidence: file:interpro/panther/PTHR11850/PTHR11850-metadata.yaml regulating gene expression patterns critical for morphogenesis, organ development, and cellular differentiation PMID:12070094 ectopic WUS and STM activities induce the expression of different downstream target genes |
| GO:0009888 tissue development | IEA GO_REF:0000117 | MODIFY | Summary: Tissue development is correct only at a very broad level. For STM, the specific supported processes are meristem structural organization, stem cell population maintenance, cytokinin biosynthesis, floral meristem fate, and carpel initiation. Reason: Replace the broad ARBA term with more specific existing STM terms rather than retaining a vague developmental parent. Proposed replacements: regulation of meristem structural organization stem cell population maintenance Supporting Evidence: PMID:12070094 STM is required to suppress differentiation throughout the meristem dome PMID:12068101 At later developmental stages, WUS promotes the level of CLV3 expression, together with STM |
| GO:0010497 plasmodesmata-mediated intercellular transport | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: The original ISS transfer comes from KNOTTED1-family evidence, and STM-specific trafficking evidence supports plasmodesmata-mediated movement as a biologically important non-core process. Reason: Retain the annotation because STM mobility is well supported, but treat it as a trafficking/regulatory property rather than the core molecular activity. Supporting Evidence: PMID:29742441 STM localizes substantially to the plasma membrane, which promotes intercellular trafficking file:ARATH/STM/STM-uniprot.txt Dynamic localization via a plasmodesmata-mediated cell-to-cell transport |
| GO:0005634 nucleus | IEA GO_REF:0000002 | ACCEPT | Summary: Nuclear localization is expected from STM's KNOX/TALE transcription factor activity and is experimentally supported by BLH-dependent nuclear import and FTIP-dependent recycling. Reason: Nucleus is the core active location for STM's transcription factor activity. Supporting Evidence: PMID:16513846 STM is targeted into the nuclear compartment through heterodimerization with BLH partner proteins PMID:29742441 This facilitates STM recycling to the nucleus |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular mapping to nucleus is correct and supported by experimental STM localization studies. Reason: Nuclear localization is core for STM as a DNA-binding transcription factor. Supporting Evidence: file:ARATH/STM/STM-uniprot.txt SUBCELLULAR LOCATION: Nucleus PMID:16513846 STM is targeted into the nuclear compartment through heterodimerization with BLH partner proteins |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: AtSubP prediction agrees with extensive experimental and curated evidence that STM localizes to the nucleus for transcriptional regulation. Reason: The prediction is supported by independent experiments, so the nuclear term is acceptable despite the computational evidence code. Supporting Evidence: PMID:16513846 STM is targeted into the nuclear compartment through heterodimerization with BLH partner proteins |
| GO:0005634 nucleus | IDA PMID:16513846 Nuclear import of the transcription factor SHOOT MERISTEMLES... | ACCEPT | Summary: Direct localization experiments show that STM nuclear import depends on heterodimerization with BLH partners. Reason: This is strong experimental support for the core location of STM activity. Supporting Evidence: PMID:16513846 STM is targeted into the nuclear compartment through heterodimerization with BLH partner proteins PMID:16513846 nuclear uptake depends on partner proteins |
| GO:0005634 nucleus | IDA PMID:29742441 FTIP-Dependent STM Trafficking Regulates Shoot Meristem Deve... | ACCEPT | Summary: FTIP3/FTIP4 regulate STM trafficking so that STM can recycle to the nucleus and maintain shoot stem cells. Reason: This experimental study directly supports nuclear localization as a functional destination of STM trafficking. Supporting Evidence: PMID:29742441 This facilitates STM recycling to the nucleus PMID:29742441 compromises nuclear localization of STM |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Cytoplasm is a supported trafficking/localization state in UniProt, but STM's core activity occurs in the nucleus. Reason: Retain as a non-core localization state associated with trafficking and cytosolic puncta. Supporting Evidence: file:ARATH/STM/STM-uniprot.txt Cytoplasm {ECO:0000269|PubMed:17965274} |
| GO:0005737 cytoplasm | IDA PMID:17965274 MPB2C, a microtubule-associated protein, regulates non-cell-... | KEEP AS NON CORE | Summary: MBP2C-dependent regulation places KNOX trafficking in cytosolic puncta at microtubules. This is a trafficking-associated state, not the primary active transcriptional compartment. Reason: Retain as non-core because it reflects regulation of STM mobility and localization rather than its DNA-binding transcription factor activity. Supporting Evidence: file:ARATH/STM/STM-uniprot.txt This shuttle is repressed by MBP2C binding in cytosolic punctae, at microtubules |
| GO:0005768 endosome | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Endosome localization is supported by UniProt mapping from the STM trafficking study, but it is a trafficking state rather than the core activity site. Reason: Retain as non-core localization tied to FTIP-regulated STM trafficking. Supporting Evidence: file:ARATH/STM/STM-uniprot.txt Endosome {ECO:0000269|PubMed:29742441} |
| GO:0005768 endosome | IDA PMID:29742441 FTIP-Dependent STM Trafficking Regulates Shoot Meristem Deve... | KEEP AS NON CORE | Summary: FTIP3/FTIP4 promote STM endosome localization and nuclear recycling in the shoot meristem. Reason: The term is supported, but it describes a trafficking intermediate rather than the core location of STM's transcriptional activity. Supporting Evidence: file:ARATH/STM/STM-uniprot.txt FTIP3 and FTIP4, which promote endosome localization (PubMed:29742441) |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Plasma membrane localization is supported in the FTIP trafficking model; loss of FTIP3/4 shifts STM substantially to the plasma membrane and increases intercellular trafficking. Reason: Retain as a non-core localization associated with STM transport through plasmodesmata. Supporting Evidence: PMID:29742441 STM localizes substantially to the plasma membrane |
| GO:0005886 plasma membrane | IDA PMID:29742441 FTIP-Dependent STM Trafficking Regulates Shoot Meristem Deve... | KEEP AS NON CORE | Summary: Direct STM trafficking evidence supports plasma membrane localization when FTIP3/4 regulation is lost or altered. Reason: This localization is relevant to trafficking but is not the core site of STM's transcriptional activity. Supporting Evidence: PMID:29742441 STM localizes substantially to the plasma membrane PMID:29742441 promotes intercellular trafficking |
| GO:0009506 plasmodesma | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Plasmodesma localization is inferred from KNOTTED1-family evidence and is consistent with STM-specific trafficking through plasmodesmata. Reason: Retain as a biologically important trafficking location, but not as the primary active site of the transcription factor function. Supporting Evidence: file:ARATH/STM/STM-uniprot.txt Dynamic localization via a plasmodesmata-mediated cell-to-cell transport |
| GO:0009506 plasmodesma | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt subcellular mapping to plasmodesma is consistent with the FTIP-dependent STM trafficking model. Reason: Retain as a trafficking-associated location, not the core nuclear transcription factor compartment. Supporting Evidence: file:ARATH/STM/STM-uniprot.txt Cell junction, plasmodesma {ECO:0000269|PubMed:29742441} |
| GO:0009506 plasmodesma | IDA PMID:29742441 FTIP-Dependent STM Trafficking Regulates Shoot Meristem Deve... | KEEP AS NON CORE | Summary: The FTIP paper supports intercellular STM trafficking, which is consistent with plasmodesmata-associated localization. Reason: The term is correct for STM mobility, but should be kept separate from the core nuclear transcription factor function. Supporting Evidence: PMID:29742441 STM localizes substantially to the plasma membrane, which promotes intercellular trafficking file:ARATH/STM/STM-uniprot.txt Cell junction, plasmodesma {ECO:0000269|PubMed:29742441} |
| GO:0015630 microtubule cytoskeleton | IDA PMID:17965274 MPB2C, a microtubule-associated protein, regulates non-cell-... | KEEP AS NON CORE | Summary: STM trafficking is regulated by MBP2C in cytosolic puncta at microtubules. This is a localization/regulatory state rather than the primary site of STM activity. Reason: Retain as non-core because it reflects MBP2C-dependent trafficking control of STM. Supporting Evidence: file:ARATH/STM/STM-uniprot.txt This shuttle is repressed by MBP2C binding in cytosolic punctae, at microtubules |
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Download this section (compressed HTML)Q: Which STM-BELL/BLH heterodimer combinations are required for specific direct transcriptional targets in central, peripheral, and boundary domains of the shoot apical meristem?
Q: Is RNA binding an experimentally demonstrable activity of Arabidopsis STM itself, or should the current RNA-binding annotation be restricted to maize KN1/MPB2C-related evidence?
Q: Which STM trafficking states are required for transcriptional function versus non-cell-autonomous signaling through plasmodesmata?
Experiment: Perform native-promoter STM ChIP-seq or CUT&RUN in STM complementation lines with and without specific BLH partners to assign direct targets to defined STM heterodimer complexes.
Hypothesis: Distinct BLH partners confer domain-specific target selection for STM in the shoot apical meristem.
Type: ChIP-seq/CUT&RUN
Experiment: Test purified Arabidopsis STM for direct RNA binding using EMSA or fluorescence anisotropy with STM mRNA and unrelated RNA controls, alongside maize KN1 and MPB2C controls.
Hypothesis: The current STM RNA-binding annotation may reflect KN1/MPB2C trafficking literature rather than a direct Arabidopsis STM RNA-binding activity.
Type: in vitro RNA-binding assay
Experiment: Use STM variants defective in BLH binding, MBP2C binding, or FTIP-dependent trafficking in stm rescue backgrounds to separate nuclear transcriptional activity from plasmodesmata-mediated mobility.
Hypothesis: STM meristem maintenance requires BLH-dependent nuclear import, while plasmodesmata-associated mobility contributes to boundary and tissue-level patterning.
Type: structure-function rescue and live imaging
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