Root ground-tissue radial patterning by the SHORT-ROOT-SCARECROW-BIRD module

Radial patterning of the Arabidopsis root ground tissue is organised by a mobile GRAS-domain transcriptional regulator. SHORT-ROOT (SHR) is transcribed in the stele but the protein moves through plasmodesmata into the single adjacent cell layer (endodermis, cortex/endodermis initial (CEI) and quiescent centre (QC)). There it is captured in the nucleus by the related GRAS protein SCARECROW (SCR), with which it forms a head-to-head heterodimer, and by BIRD/INDETERMINATE-DOMAIN (IDD) C2H2 zinc-finger transcription factors such as JACKDAW (JKD/IDD10) and MAGPIE (MGP/IDD3). The BIRD zinc fingers ZF1-ZF3 contact DNA while ZF3-ZF4 dock into a groove on SHR, so the SHR-SCR heterodimer acts as a transcriptional coregulator brought to target promoters by BIRD proteins. Nuclear retention limits SHR movement to one layer, and the SHR-SCR-BIRD complex activates SCR itself (a positive feedback loop), MGP and other BIRDs (a feed-forward loop), and the D-type cyclin CYCD6;1. CYCD6;1 binds and activates CDKB1 kinases that phosphorylate RETINOBLASTOMA-RELATED (RBR), relieving RBR repression of SCR; this nested feed-forward loop triggers the formative asymmetric periclinal division of the CEI daughter that produces separate endodermis and cortex layers. SHR-SCR also specify endodermal identity, and SCR is required cell-autonomously for QC identity, providing the niche context in which the QC transcription factor WOX5 maintains the surrounding stem cells. Middle-cortex formation later in development reuses the SHR-SCR-CYCD6;1 module.

CONCRETE Arabidopsis module. All members are grounded as GENE_PRODUCT selectors by UniProtKB accession taken from the gene folders (SHR Q9SZF7, SCR Q9M384, JKD Q700D2, MGP Q9ZWA6, CYCD6;1 Q9ZR04, WOX5 Q8H1D2). No PANTHER family ids are asserted: UniProt assigns the BIRD/IDD proteins to PTHR10593, whose official family name ("SERINE/THREONINE-PROTEIN KINASE RIO") is dominated by an unrelated member, so a family descriptor would mislead. For reference, UniProt places JKD in subfamily PTHR10593:SF231 ("PROTEIN INDETERMINATE-DOMAIN 13-RELATED") and MGP in PTHR10593:SF148 ("ZINC FINGER PROTEIN MAGPIE"), and CYCD6;1 in PTHR10177 ("CYCLINS"). These are recorded here only and are not asserted as family descriptors. Other BIRDs (BIB/IDD9, NUC/IDD8, BLJ/IDD1, IME/IDD2) and CDKB1;1/1;2 and RBR participate but have no gene reviews yet; they are named in prose only. WOX5 is modelled as an optional context part for QC identity, not as a core step of ground-tissue patterning. No GO-CAM models in gocams/index.tsv contain these proteins. SHR intercellular movement is described in the SHR gene review (proposed new term) and is represented here only in prose and as the first part. Process granularity differs between annotons on purpose. The SHR annoton reuses GO:0009956 radial pattern formation from the existing SHR review, because SHR also acts in shoot tissues (its review covers leaf development), so the general term is kept there. The JKD and MGP annotons use the root-specific child GO:0090057 root radial pattern formation, because their documented roles are confined to the root. Both SCR and JKD nuclear-capture annotons use GO:0051457 maintenance of protein location in nucleus, because both retain SHR that has already entered the nucleus.