Genome-Wide Identification, Expression and Potential Function Analysis of the ERF and DREB Subfamily Members in Tomato

Abstract

Background: APETALA2/ethylene responsive factors (AP2/ERFs) are unique regulators found in the plant kingdom that are involved in all life activity processes, including flowering, fruit ripening, floral meristem growth, and defense responses. In tomato (Solanum lycopersicum), there are 60 DREB and 80 ERF subfamily members, however, their functionality remains poorly understood.Results: In this work, the AP2 domain conserved amino acid sequences of 68 ERF proteins from 20 plant species were compared and a Multiple Em for Motif Elicitation (MEME) analysis was conducted. Results revealed that the 9th amino acid of the AP2 domain exhibited marked characteristics during the selection of DRE/CRT and/or GCC boxes as protein binding sites. Moreover, motifs near the AP2 domain may be involved in protein binding to DNA, whereas motifs far away from the AP2 domain may function as a part of the transactivation domain. Furthermore, we compared the expression levels of all ERF genes in 30 tomato organs and under biotic and abiotic stresses. Results indicated that most of 17 ERF and DREB repressor genes were highly expressed in almost all tomato organs and under some biotic and abiotic stress. The transcripts per million (TPM) value ratios of all repressor genes exceeded that of all activator genes in 16 tomato organs. Thus, it can be inferred that these repressor genes play vital roles in balancing the regulatory functions of activator genes and activator genes may also conversely compete with repressor genes to ensure normal growth, development, and defense responses in tomato.Conclusions: This work uncovered the potential functions of all ERF and DREB genes that regulate tomato growth, development, and defense responses, and considers the binding ability of the AP2 domain unique sequences with DRE/CRT and GCC boxes, as well as the relationship of unique motifs with the transactivation domain. These findings will expand upon our understanding of the functions of ERF and DREB genes in tomato.

ERF subfamily transcription factors and their function in plant responses to abiotic stresses

“…Zhang et al (2010) found that JERF1, a tomato ERF protein, significantly enhanced drought tolerance of transgenic rice through increasing the synthesis of the osmolyte proline. Besides, An et al (2020) found that MdERF38, an apple ERF protein, promoted anthocyanin biosynthesis in response to drought stress. In rice, OsERF115/AP2EREBP110 enhance drought tolerance by elevating the expression level of a proline biosynthesis P5CS1 gene (Park S. I. et al, 2021).…”

“…Lv et al (2019) found that overexpression of BpERF13 up-regulated SOD1, SOD3, POD6, POD8, CBF3 and CBF4 genes and down-regulated the accumulation of ROS to resist oxidative stress, thus enhancing the cold tolerance of birch (Betula platyphylla). Hu et al (2020) showed that overexpression of CdERF1 in bermudagrass (Cynodon dactylon) positively regulated cold response by activating cold stress-related genes PODs, CBF2 and LTPs. In transgenic Arabidopsis, heterologous expression Malus baccata MbERF11 contributed to cold stress response probably by promoting the ability to scavenge ROS (Han et al, 2020).…”

“…Ma et al (2021) found that MdERF109 promoted light-induced anthocyanin biosynthesis by directly binding to promoters of anthocyanin-related genes MdCHS, MdUFGT, and MdbHLH3 in apple. Besides, An et al (2020) showed that apple MdERF38 was able to promote the expression of anthocyanin biosynthetic genes MdDFR, MdUF3GT, MdCHI and MdCHS under drought stress. Cao et al (2021) suggested that four lily (Lilium brownii var.…”

“…(2008) shown that the Ser-15 in the AP2/ERF domain was demonstrated to be essential for its specific binding to GCC-box. Recent studies showed that some other amino acids, such as Pro-9, His-9 and Ser-9, also have important functions ( Liu et al., 2020 ; Zhang L. et al., 2022 ).…”

Genome-wide identification and expression analysis of DREB genes in alfalfa (Medicago sativa) in response to cold stress

“…To date, proteins with the AP2 domain consisting of 14 th V and 19 th E have been more likely characterized as DREBs, but those with an alanine (A)- and aspartate (D)-containing AP2 motif are assigned to ERF proteins. 27 Because the specific AP2 recognizes and binds to the DRE (dehydration-responsive element) cis -regulatory sequence in regulatory networks, such a AP2 domain represents a typical feature for DREB genes. Thus, in this study, we further used the 172 MsDREB -gene datasets for the preliminary analysis of alfalfa plant in response to cold stress.…”