The <i>EIL</i> transcription factor family in soybean: Genome‐wide identification, expression profiling and genetic diversity analysis

Li, Qing; Shen, Yanting; Guo, Luqin; Wang, Hong; Fan, Chengming; Zheng, Ye

doi:10.1002/2211-5463.12596

Cited by 10 publications

(9 citation statements)

References 60 publications

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“…Group A had the largest number with 38 EIL/EIN3 genes, followed by group B with 20, and group C with 16. The results of this study are in agreement with previous reports in other plants on classifications of these EIL/EIN3 gene groupings [30,39,42]. The EIL/EIN3 protein families in dicots and monocots were grouped in different sub-groups in our phylogenetic tree compared to previous findings.…”

Section: Phylogeny Of Eil/ein3 Memberssupporting

confidence: 93%

“…Earlier studies reported that the first part of the EIL/EIN3 gene was found to contain highly homologous sequences, which were associated with the domain of EIN3 [15]. This was similarly confirmed in several recent works [29,42]. Additionally, some changes in the motif numbers and sequences were also mentioned in the first half of the N-terminus, except in the first ~80 residues for activity [17].…”

Section: Gene Structure Analysis and Conserved Motif Analysis Of Eil/supporting

confidence: 70%

“…The molecular weight of the cotton EIN3/EIL proteins ranged from 13052.13 kDa to 77907.98 kDa (Table 1). WoLF PSORT, Protein Prowler Subcellular Localization Predictor, and TargetP1.1 Server analyses found that all of these cotton EIL/EIN3 proteins, including soybean, P. trichocarpa, and Arabidopsis EIL/EIN3 family proteins, were found to be localized in the nucleus compartment, which is in-line with their role in transcriptional regulation [39,42]. These results suggest that the EIL/EIN3 protein family may be involved in the regulation of various aspects of plant growth and development.…”

Section: Gene Identification Proceduresmentioning

confidence: 54%

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Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development

Salih

et al. 2020

Plants

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The ethylene-insensitive3-like/ethylene-insensitive3 (EIL/EIN3) protein family can serve as a crucial factor for plant growth and development under diverse environmental conditions. EIL/EIN3 protein is a form of a localized nuclear protein with DNA-binding activity that potentially contributes to the intricate network of primary and secondary metabolic pathways of plants. In light of recent research advances, next-generation sequencing (NGS) and novel bioinformatics tools have provided significant breakthroughs in the study of the EIL/EIN3 protein family in cotton. In turn, this paved the way to identifying and characterizing the EIL/EIN3 protein family. Hence, the high-throughput, rapid, and cost-effective meta sequence analyses have led to a remarkable understanding of protein families in addition to the discovery of novel genes, enzymes, metabolites, and other biomolecules of the higher plants. Therefore, this work highlights the recent advance in the genomic-sequencing analysis of higher plants, which has provided a plethora of function profiles of the EIL/EIN3 protein family. The regulatory role and crosstalk of different metabolic pathways, which are apparently affected by these transcription factor proteins in one way or another, are also discussed. The ethylene hormone plays an important role in the regulation of reactive oxygen species in plants under various environmental stress circumstances. EIL/EIN3 proteins are the key ethylene-signaling regulators and play important roles in promoting cotton fiber developmental stages. However, the function of EIL/EIN3 during initiation and early elongation stages of cotton fiber development has not yet been fully understood. The results provided valuable information on cotton EIL/EIN3 proteins, as well as a new vision into the evolutionary relationships of this gene family in cotton species.

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Section: Phylogeny Of Eil/ein3 Memberssupporting

confidence: 93%

Section: Gene Structure Analysis and Conserved Motif Analysis Of Eil/supporting

confidence: 70%

Section: Gene Identification Proceduresmentioning

confidence: 54%

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Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development

Salih

et al. 2020

Plants

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“…Comparing to N-terminal, C-terminal sequences of TaEILs showed low similarity. Therefore, it was speculated that the diversity of TaEILs came from C-terminal sequences, which was consistent with previous researches (Qing et al, 2019).…”

Section: Features Of Predicted Taeil Proteinssupporting

confidence: 88%

Genome‐wide analysis of ethylene‐insensitive3 (EIN3/EIL) in Triticum aestivum

Wen-di

Yang

et al. 2020

Crop Science

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Ethylene-insensitive proteins (EIN3/EIL) are a class of nuclear localization proteins with DNA-binding activity. EIL is an important gene family in plants, and plays key roles in the ethylene signaling pathway which regulates a broad spectrum of plant growth and development, as well as defenses to various biological and abiotic stresses. Although genome-wide analyses of EIL gene family has been carried out for several plant species, no comprehensive analysis of this family in Triticum aestivum L. has been reported so far. Furthermore, there are few scattered studies on the functions of EIL genes in wheat. It is necessary to comprehensively identify and analyze the EIL gene family in wheat. In this study, BLASTp were used to identify EIL genes in the lately released reference genome of T. aestivum. The 21 TaEIL genes were sought, which can be divided into three groups (a, b, and c) according to phylogenetic relationship. The nonsynonymous/synonymous substitution rates (Ka/Ks) value showed that three homologous pairs (TaEILb.4/TaEILb.6, TaEILa.8/TaEILa.7, and TaEILa.8/TaEILa.9) experienced strongly purifying selection. The remaining 16 homologous pairs underwent positive selection with an evolutionary acceleration. Analysis of gene structure and motif, protein features, and three-dimensional structure showed that TaEILs were similar with EILs in other species such as Arabidopsis, rice, and maize. Homology analyses of EIL in T. aestivum and its progenitors showed that EIL gene discarded some redundant genes during the domestication evolution of T. aestivum and retained some useful genes. Gene expression patterns analyses and

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“…SLIM1/EIL3 is a transcription factor (TF) that controls the S deficiency (−S) responsive gene expression, while it belongs to the plant-specific EIL family of TFs (EIL-TFs) [ 3 , 4 ]. The EIL domain is conserved among the EIL-TFs, but the N- and C-terminal regions are variable ( Figure 1 ) [ 5 ]. The best-characterized member of the EIL-TFs family is EIN3 (Ethylene-INsensitive3) which initiates downstream transcriptional cascades for ethylene responses [ 6 , 7 , 8 ].…”

Section: Introductionmentioning

confidence: 99%

The C-Terminal Region of SLIM1 Transcription Factor Is Required for Sulfur Deficiency Response

Piotrowska

Jodoi

Trang

et al. 2022

Plants

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Sulfur LIMitation1 (SLIM1) transcription factor coordinates gene expression in plants in response to sulfur deficiency (−S). SLIM1 belongs to the family of plant-specific EIL transcription factors with EIN3 and EIL1, which regulate the ethylene-responsive gene expression. The EIL domains consist of DNA binding and dimerization domains highly conserved among EIL family members, while the N- and C-terminal regions are structurally variable and postulated to have regulatory roles in this protein family, such that the EIN3 C-terminal region is essential for its ethylene-responsive activation. In this study, we focused on the roles of the SLIM1 C-terminal region. We examined the transactivation activity of the full-length and the truncated SLIM1 in yeast and Arabidopsis. The full-length SLIM1 and the truncated form of SLIM1 with a deletion of C-terminal 106 amino acids (ΔC105) transactivated the reporter gene expression in yeast when they were fused to the GAL4 DNA binding domain, whereas the deletion of additional 15 amino acids to remove the C-terminal 120 amino acids (ΔC120) eliminated such an activity, identifying the necessity of that 15-amino-acid segment for transactivation. In the Arabidopsis slim1-2 mutant, the transcript levels of SULTR1;2 sulfate transporter and the GFP expression derived from the SULTR1;2 promoter-GFP (PSULTR1;2-GFP) transgene construct were restored under −S by introducing the full-length SLIM1, but not with the C-terminal truncated forms ΔC105 and ΔC57. Furthermore, the transcript levels of −S-responsive genes were restored concomitantly with an increase in glutathione accumulation in the complementing lines with the full-length SLIM1 but not with ΔC57. The C-terminal 57 amino acids of SLIM1 were also shown to be necessary for transactivation of a −S-inducible gene, SHM7/MSA1, in a transient expression system using the SHM7/MSA1 promoter-GUS as a reporter. These findings suggest that the C-terminal region is essential for the SLIM1 activity.

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The EIL transcription factor family in soybean: Genome‐wide identification, expression profiling and genetic diversity analysis

Cited by 10 publications

References 60 publications

Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development

Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development

Genome‐wide analysis of ethylene‐insensitive3 (EIN3/EIL) in Triticum aestivum

The C-Terminal Region of SLIM1 Transcription Factor Is Required for Sulfur Deficiency Response

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