{PDOC52095}
{PS52095; FAF}
{BEGIN}
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* FANTASTIC FOUR (FAF) domain profile *
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Plant development   and  environmental  adaptation  are  governed  by  complex
regulatory networks, in which small, plant-specific proteins often function as
modulatory components.  The FANTASTIC FOUR (FAF) protein family represents one
such group   of  regulatory  proteins.  FAF  proteins,  despite  their  simple
structure, are  crucial  regulators of developmental processes. FAF genes were
first identified  in  Arabidopsis  thaliana and encode small proteins that are
highly conserved across land plants and share a FAF domain of ~50 amino acids.
Since their  initial  identification  in  Arabidopsis  thaliana,  FAF  domain-
containing proteins  have  been  linked  to shoot apical meristem maintenance,
organ initiation,  and  developmental  timing,  positioning them as modulators
that fine-tune   growth-related   signaling  pathways.  FAF  domain-containing
proteins act as context-dependent modulators whose roles depend on tissue type
and developmental  status.  The  observed cytoplasmic localization and lack of
recognizable DNA-binding domains and transcriptional activation motifs suggest
that FAF  domain-containg  proteins  are  unlikely  to  function  as classical
transcription factors  and  may  instead  act  as modulatory components within
protein complexes. FAF domain-containing proteins may act as modulators of key
developmental hubs [1].

The FAF  domain is made of two two-stranded antiparallel beta-sheets spreading
apart. A  short  alpha-helix  is  located  in  between  the  two  two-stranded
antiparallel beta-sheets [1,2].

Some proteins known to contain a FAF domain are listed below:

 - Arabidopsis  thaliana  FAF1,  FAF2,  FAF3  and  FAF4,  that influence shoot
   meristem size [3].
 - Arabidopsis  thaliana  FAF-like,  a  more  distantly  related protein which
   shares several conserved domains [3].
 - Tomato   FAF1/2a,  FAF1/2b,  FAF1/2c,  FAF3/4a  and  FAF3/4b, homologues of
   Arabidopsis FAFs  which  positively  or  negatively regulate flowering time
   [4].
 - Tomato  Cell  Size  Regulator  (CSR), mainly expressed in fruit tissues and
   vascular bundles during the fruit maturation process, which ultimately lead
   to increases in the mesocarp cell size and fruit weight [4,5].
 - Tomato CSR-like 1 to 3 [5].
 - Maize  Enhancer of ABA Co-Receptor1 (EAR1) protein, a negative regulator of
   abscisic acid  (ABA) signaling that interacts with the inhibition domain at
   the N termini of type 2C protein phosphatases (PP2Cs) [6].
 - Maize   sugary  enhancer1  (se1),  a  protein  affecting  endosperm  starch
   metabolism [7].
 - Rice  Vegetative  Cell Specific 1 (VCS1), might function in the tapetum and
   influence the generation of microspores [8].
 - Wheat TaFAF-5D.5 protein, associated with both developmental adaptation and
   heat stress responses [1].

The profile we developed covers the entire FAF domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: March 2026 / First entry.

[ 1] Jiang J., Hou Z., Wang S., Zhang Y., Li Y., Fang Z.
     "Genome-Wide Characterization of the Fantastic Four Gene Family Identifies
     TaFAF-5D.5 Associated with Growth Habit Variation in Wheat."
     Agronomy (Basel) 16:2073-4395(2026).
     DOI=10.3390/agronomy16020221
[ 2] Sigrist C.J.A.
     Unpublished observations (2026).
[ 3] Wahl V., Brand L.H., Guo Y.-L., Schmid M.
     "The FANTASTIC FOUR proteins influence shoot meristem size in
     Arabidopsis  thaliana."
     BMC Plant. Biol. 10:285-285(2010).
     PubMed=21176196; DOI=10.1186/1471-2229-10-285
[ 4] Shang L., Tao J., Song J., Wang Y., Zhang X., Ge P., Li F., Dong H.,
     Gai W., Grierson D., Ye Z., Zhang Y.
     "CRISPR/Cas9-mediated mutations of FANTASTIC FOUR gene family for
     creating early  flowering mutants in tomato."
     Plant. Biotechnol. J. 22:774-784(2024).
     PubMed=37942846; DOI=10.1111/pbi.14223
[ 5] Mu Q., Huang Z., Chakrabarti M., Illa-Berenguer E., Liu X., Wang Y.,
     Ramos A., van der Knaap E.
     "Fruit weight is controlled by Cell Size Regulator encoding a novel
     protein that  is expressed in maturing tomato fruits."
     PLoS Genet. 13:E1006930-E1006930(2017).
     PubMed=28817560; DOI=10.1371/journal.pgen.1006930
[ 6] Wang K., He J., Zhao Y., Wu T., Zhou X., Ding Y., Kong L., Wang X.,
     Wang Y., Li J., Song C.-P., Wang B., Yang S., Zhu J.-K., Gong Z.
     "EAR1 Negatively Regulates ABA Signaling by Enhancing 2C Protein
     Phosphatase  Activity."
     Plant. Cell. 30:815-834(2018).
     PubMed=29618630; DOI=10.1105/tpc.17.00875
[ 7] Zhang X., Haro von Mogel K.J., Lor V.S., Hirsch C.N., De Vries B.,
     Kaeppler H.F., Tracy W.F., Kaeppler S.M.
     "Maize sugary enhancer1 (se1) is a gene affecting endosperm starch
     metabolism."
     Proc. Natl. Acad. Sci. U. S. A. 116:20776-20785(2019).
     PubMed=31548423; DOI=10.1073/pnas.1902747116
[ 8] Wang Y., Wang T., Liu L.
     "The rice VCS1 is identified as a molecular tool to mark and visualize
     the  vegetative cell of pollen."
     Plant. Signal. Behav. 16:1924502-1924502(2021).
     PubMed=33982648; DOI=10.1080/15592324.2021.1924502

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