GRAS Family from Brachypodium

Brachypodium families updated 2023 based on Maize family rules

Required domains for GRAS family:PF03514

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The GRAS family of transcription factors are plant specific proteins whose name is derived from the first three members identified and studied: GAI (GIBBERELLIN INSENSITIVE), RGA (REPRESSOR OF GAI), and SCR (SCARECROW). Members of this family are characterized by highly conserved carboxy terminal region consisting of five motifs arranged in the order of LHR I (Leucine Heptad Repeat I), the VHIID motif, LHRII (Leucine Heptad Repeat II), the PFYRE motif and the SAW motif and a variable amino terminal region (Pysh et al., 1999). The LHRs are important for protein dimerization, whereas VHIID, PFYRE and SAW have repressor function (Itoh et al., 2002). The length and sequence variable  N-terminal domain made up of homopolymeric amino acid residues is intrinsically disordered and are involved in molecular recognition, thus members of this family act as hubs in several protein-protein interactions and thereby not only regulating processes like plant growth and development but also playing crucial role in many signaling pathways (Sun et al., 2011). DELLA subfamily consists of conserved DELLA and TVHYNP region at N-terminal and includes GAI and RGA proteins that are important regulators of gibberellin, light and jasmonate signaling (Sun TP., 2011). SCR and SHR play role in regulating root growth, root radial patterning and leaves cell proliferation (Benfy et al., 1993, Helariuttaet al.,2000,  Dhondt et al., 2010)


Eighty six GRAS family of transcription factors are present in Maize with amino acid length of 111-734 distributed into 8 subfamilies namely SCL3 (Scarecrow-like 3), HAM (HAIRY MERISTEM), LS (Lateral Suppressor), SCR (SCARECROW), DELLA, SHR (Short-root), PAT1 (Phytochrome A signal transduction 1) and LISCL (Lilium longiflorum Scarecrow-like) named after their common feature or one of the member (Guo et al., 2017). Arabidopsis, rice and sorghum consist of 34, 60 and 81 putative GRAS genes respectively divided into at least 13 subfamilies (Liu et al., 2014., Fan et al., 2021)


A Slender Rice1 (SLR1) protein identified by loss of function mutant (elongated stem, leaf sheath and blade) in rice and gain of function mutant of GAI in Arabidopsis belongs to DELLA subfamily (Ikeda et al., 2001, Peng et al., 1997). SLR1 act as a repressor of gibberellin acid signaling (GA) since its level in the nucleus changes with respect to presence or absence of GA. Domain analysis of SLR1 revealed presence of GA signal perception domain, dimer formation domain, repressor domain and regulatory domain (Itoh et al., 2002). Rice, OsSCL7 identified from transcriptomic analysis of early defense response to Magnaporthe oryzae, act as a positive regulator of defense responsive genes and its stability is affected by GF14c, a 14-3-3 protein. Also OsSCL7 mutation and overexpression resulted in developmental and growth defects implying its role in plant growth (Lue et al., 2022). A maize specific Indeterminate 1 regulator which belongs to Indeterminate domain (IDD) family of transcription factor contains highly conserved four zinc finger motifs that forms ID domain and acts as a flowering transition regulator (Colasanti et al., 2006, Colasanti et al., 1998). AtIDD interacts with DELLA subfamily and regulates the expression of genes involved in GA synthesis (GA3ox1) and signaling (SCL3) (Aoyanagi et al., 2020)


Last updated June 2023 by Ankita Abnave


Pysh LD, Wysocka-Diller JW, Camilleri C, Bouchez D, Benfey PN. The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes. Plant J. 1999 Apr;18(1):111-9. doi: 10.1046/j.1365-313x.1999.00431.x. PMID: 10341448.

Itoh H, Ueguchi-Tanaka M, Sato Y, Ashikari M, Matsuoka M. The gibberellin signaling pathway is regulated by the appearance and disappearance of SLENDER RICE1 in nuclei. Plant Cell. 2002 Jan;14(1):57-70. doi: 10.1105/tpc.010319. PMID: 11826299; PMCID: PMC150551.

Sun X, Xue B, Jones WT, Rikkerink E, Dunker AK, Uversky VN. A functionally required unfoldome from the plant kingdom: intrinsically disordered N-terminal domains of GRAS proteins are involved in molecular recognition during plant development. Plant Mol Biol. 2011 Oct;77(3):205-23. doi: 10.1007/s11103-011-9803-z. Epub 2011 Jul 6. PMID: 21732203.

Guo Y, Wu H, Li X, Li Q, Zhao X, Duan X, An Y, Lv W, An H. Identification and expression of GRAS family genes in maize (Zea mays L.). PLoS One. 2017 Sep 28;12(9):e0185418. doi: 10.1371/journal.pone.0185418. PMID: 28957440; PMCID: PMC5619761.

Liu, X., Widmer, A. Genome-wide Comparative Analysis of the GRAS Gene Family in Populus, Arabidopsis and Rice. Plant Mol Biol Rep 32, 1129–1145 (2014).

Ikeda, A., Tanaka, S., Yamaguchi, J., and Futsuhara, Y. (1999a). Character expression and mode of inheritance of a slender mutant with constitutive gibberellin-response in rice [Japanese]. Sci. Rep. Fac. Agric. Meijo Univ. 35, 7–13

Peng J, Carol P, Richards DE, King KE, Cowling RJ, Murphy GP, Harberd NP. The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses. Genes Dev. 1997 Dec 1;11(23):3194-205. doi: 10.1101/gad.11.23.3194. PMID: 9389651; PMCID: PMC316750.

Lu L, Diao Z, Yang D, Wang X, Zheng X, Xiang X, Xiao Y, Chen Z, Wang W, Wu Y, Tang D, Li S. The 14-3-3 protein GF14c positively regulates immunity by modulating the protein homoeostasis of the GRAS protein OsSCL7 in rice. Plant Cell Environ. 2022 Apr;45(4):1065-1081. doi: 10.1111/pce.14278. Epub 2022 Feb 17. PMID: 35129212.

Fan Y, Yan J, Lai D, Yang H, Xue G, He A, Guo T, Chen L, Cheng XB, Xiang DB, Ruan J, Cheng J. Genome-wide identification, expression analysis, and functional study of the GRAS transcription factor family and its response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]. BMC Genomics. 2021 Jul 6;22(1):509. doi: 10.1186/s12864-021-07848-z. PMID: 34229611; PMCID: PMC8259154.

Colasanti J, Tremblay R, Wong AY, Coneva V, Kozaki A, Mable BK. The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants. BMC Genomics. 2006 Jun 19;7:158. doi: 10.1186/1471-2164-7-158. PMID: 16784536; PMCID: PMC1586020.

Colasanti J, Yuan Z, Sundaresan V. The indeterminate gene encodes a zinc finger protein and regulates a leaf-generated signal required for the transition to flowering in maize. Cell. 1998 May 15;93(4):593-603. doi: 10.1016/s0092-8674(00)81188-5. PMID: 9604934.

Sun TP. The molecular mechanism and evolution of the GA-GID1-DELLA signaling module in plants. Curr Biol. 2011 May 10;21(9):R338-45. doi: 10.1016/j.cub.2011.02.036. PMID: 21549956.

Dhondt S, Coppens F, De Winter F, Swarup K, Merks RM, Inzé D, Bennett MJ, Beemster GT. SHORT-ROOT and SCARECROW regulate leaf growth in Arabidopsis by stimulating S-phase progression of the cell cycle. Plant Physiol. 2010 Nov;154(3):1183-95. doi: 10.1104/pp.110.158857. Epub 2010 Aug 25. PMID: 20739610; PMCID: PMC2971598.

Benfey PN, Linstead PJ, Roberts K, Schiefelbein JW, Hauser MT, Aeschbacher RA. Root development in Arabidopsis: four mutants with dramatically altered root morphogenesis. Development. 1993 Sep;119(1):57-70. doi: 10.1242/dev.119.Supplement.57. PMID: 8275864.

Helariutta Y, Fukaki H, Wysocka-Diller J, Nakajima K, Jung J, Sena G, Hauser MT, Benfey PN. The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling. Cell. 2000 May 26;101(5):555-67. doi: 10.1016/s0092-8674(00)80865-x. PMID: 10850497.

Aoyanagi T, Ikeya S, Kobayashi A, Kozaki A. Gene Regulation via the Combination of Transcription Factors in the INDETERMINATE DOMAIN and GRAS Families. Genes (Basel). 2020 Jun 2;11(6):613. doi: 10.3390/genes11060613. PMID: 32498388; PMCID: PMC7349898.





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