Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice

Abstract

Genes in the ERF family encode transcriptional regulators with a variety of functions involved in the developmental and physiological processes in plants. In this study, a comprehensive computational analysis identified 122 and 139 ERF family genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa L. subsp. japonica), respectively. A complete overview of this gene family in Arabidopsis is presented, including the gene structures, phylogeny, chromosome locations, and conserved motifs. In addition, a comparative analysis between these genes in Arabidopsis and rice was performed. As a result of these analyses, the ERF families in Arabidopsis and rice were divided into 12 and 15 groups, respectively, and several of these groups were further divided into subgroups. Based on the observation that 11 of these groups were present in both Arabidopsis and rice, it was concluded that the major functional diversification within the ERF family predated the monocot/dicot divergence. In contrast, some groups/ subgroups are species specific. We discuss the relationship between the structure and function of the ERF family proteins based on these results and published information. It was further concluded that the expansion of the ERF family in plants might have been due to chromosomal/segmental duplication and tandem duplication, as well as more ancient transposition and homing. These results will be useful for future functional analyses of the ERF family genes.

From network to phenotype: the dynamic wiring of an Arabidopsis transcriptional network induced by osmotic stress

“…However, it should be noted that the nature of the regulation was not always consistent between the DEX‐inducible in planta system and the TEA experiments. The repressing function of the literature‐described repressors ERF8 and ERF9 (Ohta et al , 2001; Nakano et al , 2006) seemed to be abolished by fusion with the GR domain, as observed in planta (Appendix Figs S3–S22) and in TEAs performed with ERF8‐GR or ERF9‐GR (Appendix Fig S24). The discrepancy is thus most likely due to the presence of the GR domain close to the EAR motif.…”

“…Half of the TFs of the putative mannitol‐responsive GRN belong to the ERF family (Appendix Table S1) (Nakano et al , 2006; Skirycz et al , 2011; Phukan et al , 2017), containing a single AP2/ERF domain that is responsible for the specific binding to GCC boxes in the promoter of their target genes (Fujimoto et al , 2000; Yang et al , 2009). Three ERF proteins, ERF8, ERF9, and ERF11, belong to group VIII and are putative transcriptional repressors, because they contain an ERF‐associated amphiphilic repression (EAR) domain (Nakano et al , 2006).…”

“…Three ERF proteins, ERF8, ERF9, and ERF11, belong to group VIII and are putative transcriptional repressors, because they contain an ERF‐associated amphiphilic repression (EAR) domain (Nakano et al , 2006). Six other stress‐induced ERFs belong to group IX: ERF‐1, ERF2, ERF5, ERF6, ERF59, and ERF98.…”

“…Six other stress‐induced ERFs belong to group IX: ERF‐1, ERF2, ERF5, ERF6, ERF59, and ERF98. ERF5 and ERF6 contain an additional motif, CMIX‐5, which is a predicted phosphorylation site (Fujimoto et al , 2000; Nakano et al , 2006). The last ERF protein part of the putative mannitol‐induced network, RAP2.6L, belongs to group X (Nakano et al , 2006).…”

“…ERF5 and ERF6 contain an additional motif, CMIX‐5, which is a predicted phosphorylation site (Fujimoto et al , 2000; Nakano et al , 2006). The last ERF protein part of the putative mannitol‐induced network, RAP2.6L, belongs to group X (Nakano et al , 2006). Seven members of the proposed GRN are part of the WRKY TF family: WRKY6, WRKY15, WRKY28, WRKY30, WRKY33, WRKY40, and WRKY48, which contain a conserved sequence (WRKYGQK) followed by a zinc finger motif, enabling the binding to DNA at the position of a W‐box TTGAC(C/T) (Wu et al , 2005).…”