Function Analysis of the ERF and DREB Subfamilies in Tomato Fruit Development and Ripening

Zhang, Li; Chen, Lijing; Shengqun, Pang; Zheng, Qun; Quan, Shaowen; Liu, YuFeng; Xu, Tongyu; Liu, YuDong; Qi, Mingfang

doi:10.3389/fpls.2022.849048

Cited by 16 publications

(13 citation statements)

References 77 publications

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“…In addition, Liu et al (2006) indicated that Ala-37 was reported to play a key role in binding to both GCC-box and DRE, while Sun et al (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 Zhang L. et al, 2022).…”

Section: Figurementioning

confidence: 99%

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

Zhang

et al. 2022

Front. Plant Sci.

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Ethylene Responsive Factor (ERF) subfamily comprise the largest number of proteins in the plant AP2/ERF superfamily, and have been most extensively studied on the biological functions. Members of this subfamily have been proven to regulate plant resistances to various abiotic stresses, such as drought, salinity, chilling and some other adversities. Under these stresses, ERFs are usually activated by mitogen-activated protein kinase induced phosphorylation or escape from ubiquitin-ligase enzymes, and then form complex with nucleic proteins before binding to cis-element in promoter regions of stress responsive genes. In this review, we will discuss the phylogenetic relationships among the ERF subfamily proteins, summarize molecular mechanism how the transcriptional activity of ERFs been regulated and how ERFs of different subgroup regulate the transcription of stress responsive genes, such as high-affinity K+ transporter gene PalHKT1;2, reactive oxygen species related genes LcLTP, LcPrx, and LcRP, flavonoids synthesis related genes FtF3H and LhMYBSPLATTER, etc. Though increasing researches demonstrate that ERFs are involved in various abiotic stresses, very few interact proteins and target genes of them have been comprehensively annotated. Hence, future research prospects are described on the mechanisms of how stress signals been transited to ERFs and how ERFs regulate the transcriptional expression of stress responsive genes.

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Section: Figurementioning

confidence: 99%

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

Zhang

et al. 2022

Front. Plant Sci.

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“…The AP2/ERF superfamily TFs have been identified in diverse plant species, including Arabidopsis thaliana [ 5 ], wheat ( Triticum turgidum ) [ 8 ], peanut ( Arachis hypogaea L.) [ 9 ], tomato ( Lycopersicon esculentum Miller) [ 10 ], common andrographis ( Andrographis paniculate ) [ 11 ], dark jute ( Corchorus olitorius L.) [ 12 ], and Chinese cherry ( Prunus pseudocerasus ) [ 13 ]. The AP2 subfamily binds to the GCAC(A/G)N(A/T)TCCC(A/G)ANG(C/T) element and has an essentially important impact on reproductive organ development, including the flower, ovule, spikelet, seed, floral organ identity, and meristem maintenance [ 2 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of AP2/ERF Superfamily Genes in Juglans mandshurica and Expression Analysis under Cold Stress

Zhao

Xie

Zhang

et al. 2022

IJMS

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Juglans mandshurica has strong freezing resistance, surviving temperatures as low as −40 °C, making it an important freeze tolerant germplasm resource of the genus Juglans. APETALA2/ethylene responsive factor (AP2/ERF) is a plant-specific superfamily of transcription factors that regulates plant development, growth, and the response to biotic and abiotic stress. In this study, phylogenetic analysis was used to identify 184 AP2/ERF genes in the J. mandshurica genome, which were classified into five subfamilies (JmAP2, JmRAV, JmSoloist, JmDREB, and JmERF). A significant amount of discordance was observed in the 184 AP2/ERF genes distribution of J. mandshurica throughout its 16 chromosomes. Duplication was found in 14 tandem and 122 segmental gene pairs, which indicated that duplications may be the main reason for JmAP2/ERF family expansion. Gene structural analysis revealed that 64 JmAP2/ERF genes contained introns. Gene evolution analysis among Juglandaceae revealed that J. mandshurica is separated by 14.23 and 15 Mya from Juglans regia and Carya cathayensis, respectively. Based on promoter analysis in J. mandshurica, many cis-acting elements were discovered that are related to light, hormones, tissues, and stress response processes. Proteins that may contribute to cold resistance were selected for further analysis and were used to construct a cold regulatory network based on GO annotation and JmAP2/ERF protein interaction network analysis. Expression profiling using qRT‒PCR showed that 14 JmAP2/ERF genes were involved in cold resistance, and that seven and five genes were significantly upregulated under cold stress in female flower buds and phloem tissues, respectively. This study provides new light on the role of the JmAP2/ERF gene in cold stress response, paving the way for further functional validation of JmAP2/ERF TFs and their application in the genetic improvement of Juglans and other tree species.

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“…The conserved amino acid analysis revealed that valine (V) is replaced by isoleucine (I) at the 14th position due to their same chemical structure, polarity, and characteristics in three Sl DREB genes. Both are aliphatic, non-polar, and hydrophobic, whereas glutamic acid (E) is being replaced by V, Q, D, H, L, and A at the 19th position ( Zhang et al, 2022 ). The genome-wide analysis discovered the presence of 58 Sl DREB genes, which can vary in numbers in different plants due to the variance in genome sizes and genes present in their genome.…”

Section: Discussionmentioning

confidence: 99%

“…Other genes that were downregulated or not expressed under heat and drought stress might be involved in other abiotic stresses, developmental mechanisms, and the regulation of several stress-resistant genes involved in biotic responses. Previous studies on expression analysis exhibit the role of DREB genes in fruit development and ripening ( Zhang et al, 2022 ). Overall, the present study data illustrates the comprehensive interactive networks of Sl DREBs with various other stress-responsive proteins associated with the regulation of development, growth, and stress tolerance processes in tomato.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum

et al. 2022

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Tomato is a drought-sensitive crop which has high susceptibility to adverse climatic changes. Dehydration-responsive element-binding (DREB) are significant plant transcription factors that have a vital role in regulating plant abiotic stress tolerance by networking with DRE/CRT cis-regulatory elements in response to stresses. In this study, bioinformatics analysis was performed to conduct the genome-wide identification and characterization of DREB genes and promoter elements in Solanum lycopersicum. In genome-wide coverage, 58 SlDREB genes were discovered on 12 chromosomes that justified the criteria of the presence of AP2 domain as conserved motifs. Intron–exon organization and motif analysis showed consistency with phylogenetic analysis and confirmed the absence of the A3 class, thus dividing the SlDREB genes into five categories. Gene expansion was observed through tandem duplication and segmental duplication gene events in SlDREB genes. Ka/Ks values were calculated in ortholog pairs that indicated divergence time and occurrence of purification selection during the evolutionary period. Synteny analysis demonstrated that 32 out of 58 and 47 out of 58 SlDREB genes were orthologs to Arabidopsis and Solanum tuberosum, respectively. Subcellular localization predicted that SlDREB genes were present in the nucleus and performed primary functions in DNA binding to regulate the transcriptional processes according to gene ontology. Cis-acting regulatory element analysis revealed the presence of 103 motifs in 2.5-kbp upstream promoter sequences of 58 SlDREB genes. Five representative SlDREB proteins were selected from the resultant DREB subgroups for 3D protein modeling through the Phyre2 server. All models confirmed about 90% residues in the favorable region through Ramachandran plot analysis. Moreover, active catalytic sites and occurrence in disorder regions indicated the structural and functional flexibility of SlDREB proteins. Protein association networks through STRING software suggested the potential interactors that belong to different gene families and are involved in regulating similar functional and biological processes. Transcriptome data analysis has revealed that the SlDREB gene family is engaged in defense response against drought and heat stress conditions in tomato. Overall, this comprehensive research reveals the identification and characterization of SlDREB genes that provide potential knowledge for improving abiotic stress tolerance in tomato.

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Function Analysis of the ERF and DREB Subfamilies in Tomato Fruit Development and Ripening

Cited by 16 publications

References 77 publications

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

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

Genome-Wide Identification of AP2/ERF Superfamily Genes in Juglans mandshurica and Expression Analysis under Cold Stress

Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum

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