GRF Family from Brachypodium

Brachypodium families updated 2023 based on Maize family rules

Required domains for GRF family:PF08879PF08880

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The rice gene, GROWTH-REGULATING FACTOR1 (OsGRF1), was the first member of this family to be cloned and it encodes a transcription factor that plays a regulatory role in stem elongation (van der Knaap et al. 2000). It was identified in a search for genes that are differentially expressed in the intercalary meristem of deepwater rice (Oryza sativa L.) internodes in response to gibberellin (GA).  Related transcription factors contain two conserved domains.  The first domain is named a WRC domain (PF08879), named after the conserved Trp-Arg-Cys motif, contains two distinctive features: a putative nuclear localisation signal and a zinc-finger motif (C3H). It is suggested that the WRC domain functions in DNA binding.  The second domain, the QLQ domain (PF08880) is named after a conserved Gln, Leu, Gln motif. The QLQ domain is found at the N-terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. This domain has thus been postulated to be involved in mediating protein interactions.

The GRF gene family of Arabidopsis thaliana (AtGRF), comprises nine members. The deduced AtGRF proteins contain the same characteristic regions--the QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys) domains--as do OsGRF1 and related proteins in rice. Most of the AtGRF genes are strongly expressed in actively growing and developing tissues, such as shoot tips, flower buds, and roots, but weakly in mature stem and leaf tissues. Overexpression of AtGRF1 and AtGRF2 resulted in larger leaves and cotyledons, as well as in delayed bolting of the inflorescence stem when compared to wild-type plants. In contrast, triple insertional null mutants of AtGRF1AtGRF3 had smaller leaves and cotyledons, whereas single mutants displayed no changes in phenotype and double mutants displayed only minor ones. The alteration of leaf growth in overexpressors and triple mutants was based on an increase or decrease in cell size, respectively. These results indicate that AtGRF proteins play a role in the regulation of cell expansion in leaf and cotyledon tissues (Kim et al 2003).

Since the initial studies of GRFs, a crucial regulatory module - consisting of microRNA miR396, GROWTH REGULATING FACTORS (GRFs) and GRF-INTERACTING FACTORS (GIFs) - has been shown to control growth of multiple tissues and organs in a variety of species. Research has expanded the knowledge of miR396-GRF/GIF function to crops, where it affects agronomically important traits, and highlighted its role in coordinating growth with endogenous and environmental factors. Special properties make the miR396-GRF/GIF system highly efficient in growth regulation and a promising target for improving plant yield (Nelissen et al., 2012, Liebsch et al., 2020).

A genome wide study, identified and classified 17 ZmGRFs, 10 SiGRFs, 4 ZmGIFs and 3 SiGIFs in maize (Zea mays L.) and foxtail millet (Setaria italica L.). Many ABREs (Abscisic Acid-responsive elements) were present in the promoter regions of GRFs by analysis, and the expression levels of ZmGRF4, 9, 12, 14 and ZmGIF2 were associated with the Abscisic Acid (ABA) response. Furthermore, ZmGRF9 showed collinearity with AtGRF5 between Arabidopsis and maize. ZmGRF9 conservatively interacts with ZmGIF 2, 3, and i. As a result, we systematically identified GRF and GIF family members, analyzed the regulatory network, and found that exogenous ABA inhibited the expression of GRFs, regulating responses to stress in the environment (Qin et al., 2022).

In maize the ZmGRF10 protein retains the N-terminal QLQ and WRC domains, the characteristic regions as protein-interacting and DNA-binding domains, respectively. However, it lacks nearly the entire C-terminal domain, the regions executing transactivation activity. Consistently, ZmGRF10 protein maintains the ability to interact with GRF-interacting factors (GIFs) proteins, but lacks transactivation activity. Overexpression of ZmGRF10 in maize led to a reduction in leaf size and plant height through decreasing cell proliferation, whereas the yield-related traits were not affected. Transcriptome analysis revealed that multiple biological pathways were affected by ZmGRF10 overexpression, including a few transcriptional regulatory genes, which have been demonstrated to have important roles in controlling plant growth and development. It has been proposed that ZmGRF10 aids in fine-tuning the homeostasis of the GRF-GIF complex in the regulation of cell proliferation (Wu et al., 2014).

ZmGRF4, ZmGRF10 and ZmGRF17 were subjected to CRISPR-cas9 mutation and it was found that mutations of ZmGRF10 and ZmGRF4 were associated with increases in the final leaf length of leaf 3 (FLL3) (Lorenzo et al., 2023).

Last updated June 2023 by John Gray


van der Knaap E, Kim JH, Kende H. A novel gibberellin-induced gene from rice and its potential regulatory role in stem growth. Plant Physiol. 2000 Mar;122(3):695-704. doi: 10.1104/pp.122.3.695. PMID: 10712532; PMCID: PMC58904.

Kim JH, Choi D, Kende H. The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis. Plant J. 2003 Oct;36(1):94-104. doi: 10.1046/j.1365-313x.2003.01862.x. PMID: 12974814.

Qin L, Chen H, Wu Q, Wang X. Identification and exploration of the GRF and GIF families in maize and foxtail millet. Physiol Mol Biol Plants. 2022 Sep;28(9):1717-1735. doi: 10.1007/s12298-022-01234-z. Epub 2022 Oct 10. PMID: 36387975; PMCID: PMC9636355.

Wu L, Zhang D, Xue M, Qian J, He Y, Wang S. Overexpression of the maize GRF10, an endogenous truncated growth-regulating factor protein, leads to reduction in leaf size and plant height. J Integr Plant Biol. 2014 Nov;56(11):1053-63. doi: 10.1111/jipb.12220. Epub 2014 Jul 31. PMID: 24854713.

Liebsch D, Palatnik JF. MicroRNA miR396, GRF transcription factors and GIF co-regulators: a conserved plant growth regulatory module with potential for breeding and biotechnology. Curr Opin Plant Biol. 2020 Feb;53:31-42. doi: 10.1016/j.pbi.2019.09.008. Epub 2019 Nov 11. PMID: 31726426.

Nelissen H, Rymen B, Jikumaru Y, Demuynck K, Van Lijsebettens M, Kamiya Y, Inzé D, Beemster GT. A local maximum in gibberellin levels regulates maize leaf growth by spatial control of cell division. Curr Biol. 2012 Jul 10;22(13):1183-7. doi: 10.1016/j.cub.2012.04.065. Epub 2012 Jun 7. Erratum in: Curr Biol. 2012 Jul

Lorenzo CD, Debray K, Herwegh D, Develtere W, Impens L, Schaumont D, Vandeputte W, Aesaert S, Coussens G, De Boe Y, Demuynck K, Van Hautegem T, Pauwels L, Jacobs TB, Ruttink T, Nelissen H, Inzé D. BREEDIT: a multiplex genome editing strategy to improve complex quantitative traits in maize. Plant Cell. 2023 Jan 2;35(1):218-238. doi: 10.1093/plcell/koac243. Erratum in: Plant Cell. 2023 Mar 15;35(3):1160. PMID: 36066192; PMCID: PMC9806654.



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