Volume 8, Issue 7, Pages 998-1010 (July 2015) Growth-Regulating Factors (GRFs): A Small Transcription Factor Family with Important Functions in Plant Biology  Mohammad Amin Omidbakhshfard, Sebastian Proost, Ushio Fujikura, Bernd Mueller-Roeber  Molecular Plant  Volume 8, Issue 7, Pages 998-1010 (July 2015) DOI: 10.1016/j.molp.2015.01.013 Copyright © 2015 The Author Terms and Conditions

Figure 1 GRFs Have Diverse Growth-Related Functions. Graphic summary of the known biological functions reported for GRFs from eudicot and monocot species. References to the processes and genes mentioned are given in the main text. Gene names are shown in italics. Reported interactions between GRFs and GIFs at the protein level (revealed by, e.g., yeast two-hybrid or BiFC studies) or at the genetic level are indicated by a black triangle. Arrow-ending and T-ending lines indicate positive and negative gene regulatory interactions, respectively. Molecular Plant 2015 8, 998-1010DOI: (10.1016/j.molp.2015.01.013) Copyright © 2015 The Author Terms and Conditions

Figure 2 The miR396/GRF Regulatory Module. MiR396 targets various GRF transcripts, thereby negatively regulating their abundance. The expression of miR396 itself is positively regulated by upstream TCP transcription factors and is enhanced by various types of abiotic stresses, which modulates GRF transcript abundance. Furthermore, GRFs may control miR396 transcript levels (and the expression of other GRFs, see Hewezi and Baum, 2012), although the underlying molecular details are unknown. TCP4 affects the expression levels of some GRFs and GIF1 independent of miRNA396 (Rodriguez et al., 2010). At the protein level, GRFs interact with GIFs to control growth-related processes (see Figure 1). Note that several, but not all GRFs are miR396 targets. Molecular Plant 2015 8, 998-1010DOI: (10.1016/j.molp.2015.01.013) Copyright © 2015 The Author Terms and Conditions

Figure 3 Phylogenetic Tree of the GRF Genes in PLAZA 3.0 Dicots. The multiple sequence alignment, edited with partial and outlier genes removed, was obtained for gene family HOM03D000374 from PLAZA 3.0 dicots (Proost et al., 2015) and the tree was constructed using MEGA5 (Tamura et al., 2011). As can be seen, the GRF gene family can be subdivided into six groups which were already present in the ancestor of the flowering plants. By superimposing block duplicates (also derived from PLAZA 3.0 Dicots) on the tree topology, it can be seen that in eudicots groups IV and V expanded through the whole-genome triplication in the ancestor of the eudicots (yellow stars). Similarly, albeit more recently, the GRFs in rice and maize expanded. Within some species (such as poplar and soybean), additional large-scale duplications followed by retention of the duplicates resulted in further expansions. The genes included in each group are listed in Supplemental Table 1. Individual genes, some of which have reported functions, are highlighted. The bar indicates the branch length (over which 0.2 substitutions per site are expected). Molecular Plant 2015 8, 998-1010DOI: (10.1016/j.molp.2015.01.013) Copyright © 2015 The Author Terms and Conditions

Figure 4 Domain Composition of GRFs. The majority of the 331 GRFs in PLAZA 3.0 have both the characteristic QLQ and WRC domains. A sequence motif was created using the multiple sequence alignment in PLAZA and WebLogo (http://weblogo.berkeley.edu/) to show the core QLQ and WRC motifs along with highly conserved flanking regions. In the extended WRC domain, three cysteine residues in combination with a histidine form a C3H DNA binding domain. Molecular Plant 2015 8, 998-1010DOI: (10.1016/j.molp.2015.01.013) Copyright © 2015 The Author Terms and Conditions