FAMA (bHLH097) is a nuclear basic helix-loop-helix transcription factor of the stomatal-lineage subgroup Ia (with SPEECHLESS and MUTE) that acts at the final step of stomatal development. Expressed transiently in guard mother cells (GMCs) and young guard cells, FAMA heterodimerizes with the broadly expressed group IIIb bHLHs SCREAM/ICE1 and SCRM2 to drive guard cell differentiation and to halt proliferative divisions so that each GMC divides only once, symmetrically, to form a pair of guard cells. FAMA acts as a transcriptional activator of guard-cell genes and also represses cell-cycle genes; through an LxCxE motif it binds RETINOBLASTOMA-RELATED (RBR), recruiting RBR and Polycomb-associated repression to the promoters of stomatal stem-cell regulators (such as SPCH) to make guard cell fate irreversible. fama mutants form tumour-like stacks of small, undifferentiated guard-cell-like cells, while ectopic FAMA expression confers guard cell character. FAMA acts redundantly with the MYB factors FOUR LIPS and MYB88 in restricting GMC division.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping of the bHLH domain to DNA-binding transcription factor activity. Reason: Core molecular function of FAMA, consistent with nuclear localization, a conserved basic DNA-binding region and transcriptional activation activity. Supporting Evidence: PMID:17088607 FAMA was a robust activator of GUS activity, indicating that it can act as a transcriptional activator |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | ACCEPT | Summary: Classification as a bHLH transcription factor in a genome-wide comparative survey. Reason: Consistent with experimental evidence for FAMA transcriptional activity. |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:12679534 The basic helix-loop-helix transcription factor family in pl... | ACCEPT | Summary: Classification as a bHLH transcription factor (bHLH097) in the plant bHLH family survey. Reason: Consistent with experimental evidence for FAMA transcriptional activity. |
| GO:0005515 protein binding | IPI PMID:24571519 Deep functional redundancy between FAMA and FOUR LIPS in sto... | MODIFY | Summary: FAMA interacts with RETINOBLASTOMA-RELATED (RBR1, Q9LKZ3). Reason: The FAMA-RBR interaction recruits the RBR transcriptional co-regulator to stomatal stem-cell gene promoters; transcription coregulator binding is the informative molecular function. Proposed replacements: transcription coregulator binding Supporting Evidence: PMID:24571519 Here we show that these overlapping functions are likely to also involve interactions between FLP and FAMA with the RETINOBLASTOMA-RELATED (RBR) protein. |
| GO:0005515 protein binding | IPI PMID:25303364 Irreversible fate commitment in the Arabidopsis stomatal lin... | MODIFY | Summary: FAMA binds RBR in vivo and in vitro through its LxCxE motif. Reason: As above; the LxCxE-dependent binding of the RBR co-regulator is the mechanism by which FAMA enforces irreversible guard cell fate. Proposed replacements: transcription coregulator binding Supporting Evidence: PMID:25303364 FAMA interacts with RBR in vivo and in vitro through its LxCxE motif. |
| GO:0005515 protein binding | IPI PMID:25303364 Irreversible fate commitment in the Arabidopsis stomatal lin... | MODIFY | Summary: FAMA binds RBR in vivo and in vitro through its LxCxE motif. Reason: As above; the LxCxE-dependent binding of the RBR co-regulator is the mechanism by which FAMA enforces irreversible guard cell fate. Proposed replacements: transcription coregulator binding Supporting Evidence: PMID:25303364 FAMA interacts with RBR in vivo and in vitro through its LxCxE motif. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of nuclear localization for the SPCH/MUTE/FAMA clade. Reason: FAMA-GFP fusions are nuclear. Supporting Evidence: PMID:17088607 Both N- and C-terminal fusions of GFP to FAMA were predominantly nuclear localized |
| GO:0005634 nucleus | IDA PMID:17088607 Arabidopsis FAMA controls the final proliferation/differenti... | ACCEPT | Summary: FAMA-GFP fusions localize to the nucleus. Reason: Direct evidence. Supporting Evidence: PMID:17088607 Both N- and C-terminal fusions of GFP to FAMA were predominantly nuclear localized |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location mapping. Reason: Consistent with experimental evidence. |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: Sequence-model prediction of nuclear localization. Reason: Consistent with experimental evidence. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA prediction of regulation of DNA-templated transcription. Reason: Correct; FAMA both activates and represses target genes. |
| GO:0010052 guard cell differentiation | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping (FAMA-specific family) to guard cell differentiation. Reason: Correct; FAMA is the terminal regulator of guard cell differentiation. |
| GO:0010052 guard cell differentiation | IMP PMID:17088607 Arabidopsis FAMA controls the final proliferation/differenti... | ACCEPT | Summary: fama mutants fail to differentiate guard cells and form stacks of GMC-like cells. Reason: Core biological process with direct genetic evidence. Supporting Evidence: PMID:17088607 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. |
| GO:0010052 guard cell differentiation | IMP PMID:24654956 Arabidopsis guard cell integrity involves the epigenetic sta... | ACCEPT | Summary: FAMA expression confers and stabilizes guard cell identity. Reason: Consistent with the core role. Supporting Evidence: PMID:24654956 Arabidopsis guard cell (GC) fate is conferred via a transient pulse of expression of FAMA that encodes a bHLH transcription factor. |
| GO:0010374 stomatal complex development | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of stomatal complex development for the SPCH/MUTE/FAMA clade. Reason: Correct; the more specific guard cell differentiation is also annotated. Supporting Evidence: PMID:17183267 Together, SPCH, MUTE and FAMA bHLH proteins control stomatal development at three consecutive steps |
| GO:0010377 guard cell fate commitment | IGI PMID:25303364 Irreversible fate commitment in the Arabidopsis stomatal lin... | ACCEPT | Summary: Disrupting the FAMA-RBR interaction reveals RBR's role in enforcing guard cell fate commitment. Reason: FAMA-RBR module makes guard cell differentiation irreversible; a core aspect of FAMA function. Supporting Evidence: PMID:25303364 We found that irreversible differentiation of guard cells involves RETINOBLASTOMA-RELATED (RBR) recruitment to regulatory regions of master regulators of stomatal initiation, facilitated through interaction with a terminal stomatal lineage transcription factor, FAMA. |
| GO:0010444 guard mother cell differentiation | IMP PMID:24571519 Deep functional redundancy between FAMA and FOUR LIPS in sto... | KEEP AS NON CORE | Summary: FAMA with FLP/MYB88 enforces a single symmetric GMC division. Reason: FAMA acts in the GMC to restrict its division and promote guard cell fate; the GMC-differentiation framing is valid but secondary to guard cell differentiation. Supporting Evidence: PMID:24571519 The bHLH transcription factor FAMA, along with the paralogous MYB genes, FOUR LIPS (FLP) and MYB88 all ensure that Arabidopsis stomata contain just two guard cells (GCs) by enforcing a single symmetric precursor cell division before stomatal maturity. |
| GO:0045597 positive regulation of cell differentiation | IMP PMID:17088607 Arabidopsis FAMA controls the final proliferation/differenti... | ACCEPT | Summary: FAMA promotes guard cell differentiation; ectopic FAMA confers stomatal character. Reason: Correct, general parent of FAMA's specific role. Supporting Evidence: PMID:17088607 Ectopic FAMA expression is also sufficient to confer stomatal character. |
| GO:0045893 positive regulation of DNA-templated transcription | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of positive regulation of transcription. Reason: FAMA acts as a transcriptional activator in protoplast assays. Supporting Evidence: PMID:17088607 FAMA was a robust activator of GUS activity, indicating that it can act as a transcriptional activator |
| GO:0045893 positive regulation of DNA-templated transcription | IDA PMID:17088607 Arabidopsis FAMA controls the final proliferation/differenti... | ACCEPT | Summary: Protoplast GAL4 reporter assay shows FAMA transcriptional activation. Reason: Direct evidence. Supporting Evidence: PMID:17088607 FAMA was a robust activator of GUS activity, indicating that it can act as a transcriptional activator |
| GO:0046983 protein dimerization activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping of the bHLH domain to protein dimerization activity. Reason: FAMA functions as a heterodimer with SCRM/ICE1 and SCRM2; the more specific heterodimerization activity is used in core functions. Supporting Evidence: PMID:18641265 Similarly, three stomatal bHLHs, SPCH, MUTE, and FAMA, that exhibit transient expression within a specific precursor state of the stomatal cell lineage function as heterodimers with broadly expressed ICE1. |
| GO:0051782 negative regulation of cell division | IMP PMID:17088607 Arabidopsis FAMA controls the final proliferation/differenti... | ACCEPT | Summary: fama precursors undergo extra symmetric divisions. Reason: Halting GMC proliferation is an integral part of FAMA's terminal differentiation function. Supporting Evidence: PMID:17088607 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. |
| GO:0090547 response to low humidity | IEP PMID:22442411 Low relative humidity triggers RNA-directed de novo DNA meth... | KEEP AS NON CORE | Summary: FAMA becomes methylated and transcriptionally repressed under low relative humidity. Reason: An expression response of the FAMA locus to an environmental condition; does not describe the function of the FAMA protein. Supporting Evidence: PMID:22442411 two genes in the stomatal development pathway, SPEECHLESS and FAMA, become de novo cytosine methylated and transcriptionally repressed |
| GO:0046982 protein heterodimerization activity | IPI PMID:18641265 SCREAM/ICE1 and SCREAM2 specify three cell-state transitiona... | NEW | Summary: FAMA forms heterodimers with SCREAM/ICE1 and SCRM2. Reason: Direct interaction data and genetics show FAMA acts as a heterodimer with SCRM-family bHLHs; more informative than the IEA protein dimerization activity. Supporting Evidence: PMID:18641265 Here, we identify two paralogous proteins, SCREAM (SCRM) and SCRM2, which directly interact with and specify the sequential actions of SPCH, MUTE, and FAMA. |
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Download this section (compressed HTML)Q: Which FAMA target genes are directly activated versus repressed, and does the FAMA-SCRM heterodimer bind a distinct E-box variant from SPCH-SCRM and MUTE-SCRM?
Q: Is FAMA itself a target of MPK3/MPK6 phosphorylation via SCRM's KiDoK docking motif, as SPCH is?
Experiment: ChIP-seq of FAMA in a fama mutant complemented with an LxCxE-mutant FAMA to separate RBR-dependent stable repression of stem-cell genes from FAMA's direct transcriptional activation of guard-cell genes.
Type: ChIP-seq / genetic complementation
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