AP2/ERF-AP2 Family from Maize

Required domains for AP2/ERF-AP2 family:PF00847

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In plants, the APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily is one of the largest families of plant TFs and were thought to be unique to the plant lineage. However, they are distantly related to homing endonucleases genes (HEGs) that reside in group-I self-splicing introns and it has been postulated that they evolved by horizontal transfer from a chloroplast endosymbiont in early plant evolution (Wessler 2005).

The AP2/ERF superfamily proteins contain at least one highly conserved AP2/ERF DNA-binding domain comprising 40–70 amino acid residues. It can be divided into three distinct families according to the number and similarity of AP2/ERF DNA-binding domains, namely the AP2 family, the ERF family (including two subfamilies ERF and DREB) and the RAV (Related to ABI3/VP) family. As transcription factors, AP2/ERFs regulate genes involved in diverse biological processes such as growth, development (floral organ and epidermal cell identity), hormone and stress responses through several mechanisms including transcriptional and post-translational control

In maize, a genomic survey has revealed a total of 214 genes encoding ZmAP2/ERF proteins with at least one complete AP2/ERF domain according to the (RefGen_v4) version of the maize B73 genome (Zhang et al., 2022). Of these 44 were placed in the AP2 family 166 in the ERF family and 4 in the RAV family. The number of the introns in the AP2 family genes was larger than that in the genes of two other families. However the numbers reported included multiple transcripts from individual genes and therefore underestimated the total number of family members..

A more recent genomic survey (that did not reference the Zhang et al., 2022 paper) reported 229 AP2/ERF genes in the latest (B73 RefGen_v5) maize reference genome.  These were categorized into 5 clades, including 27 AP2 (APETALA2), 5 RAV (Related to ABI3/VP), 89 DREB (dehydration responsive element binding), 105 ERF (ethylene responsive factors), and a soloist (Cheng et al., 2023).

AP2 Family: The AP2 family proteins possess two repeated AP2 domains (PF00847), the ERF family proteins only share a single AP2 domain (PF04404) and a conserved WLG-motif, while the RAV family proteins contain an AP2 domain as well as an additional B3 DNA-binding domain - a plant-specific DNA-binding domain that is conserved within other transcription factors (see also the ABI3-VP1 family of TFs).  The maize EREB110 protein (Zm00001eb355240, rap2.7 ortholog) has been implicated in brace root development and is a target of miR172.  A maize transposon insert mutant RAP2.7-Mu defective in ZmRAP2.7 expression revealed a decreased number of brace roots but not crown roots (Li et al., 2019).

Last updated June 2023 by John Gray


Wessler SR. Homing into the origin of the AP2 DNA binding domain. Trends Plant Sci. 2005 Feb;10(2):54-6. doi: 10.1016/j.tplants.2004.12.007. PMID: 15708341.

Kagaya Y, Ohmiya K, Hattori T. RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. Nucleic Acids Res. 1999 Jan 15;27(2):470-8. doi: 10.1093/nar/27.2.470. PMID: 9862967; PMCID: PMC148202.

Xie Z, Nolan TM, Jiang H, Yin Y. AP2/ERF Transcription Factor Regulatory Networks in Hormone and Abiotic Stress Responses in Arabidopsis. Front Plant Sci. 2019 Feb 28;10:228. doi: 10.3389/fpls.2019.00228. PMID: 30873200; PMCID: PMC6403161.

Zhang J, Liao J, Ling Q, Xi Y, Qian Y. Genome-wide identification and expression profiling analysis of maize AP2/ERF superfamily genes reveal essential roles in abiotic stress tolerance. BMC Genomics. 2022 Feb 12;23(1):125. doi: 10.1186/s12864-022-08345-7. PMID: 35151253; PMCID: PMC8841118.

Cheng C, An L, Li F, Ahmad W, Aslam M, Ul Haq MZ, Yan Y, Ahmad RM. Wide-Range Portrayal of AP2/ERF Transcription Factor Family in Maize (Zea mays L.) Development and Stress Responses. Genes (Basel). 2023 Jan 11;14(1):194. doi: 10.3390/genes14010194. PMID: 36672935; PMCID: PMC9859492.

Li J, Chen F, Li Y, Li P, Wang Y, Mi G, Yuan L. ZmRAP2.7, an AP2 Transcription Factor, Is Involved in Maize Brace Roots Development. Front Plant Sci. 2019 Jul 4;10:820. doi: 10.3389/fpls.2019.00820. PMID: 31333689; PMCID: PMC6621205.




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