Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.)

Abstract

The C2H2 zinc finger protein (C2H2-ZFP) transcription factor family regulates the expression of a wide variety of genes in response to various developmental processes or abiotic stresses; however, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum). In this study, a total of 104 C2H2-ZFs were identified in an uneven distribution across the entire tomato genome, and include seven segmental duplication events. Based on their phylogenetic relationships, these genes were clustered into nine distinct categories analogous to those in Arabidopsis thaliana. High similarities were found between the exon–intron structures and conserved motifs of the genes within each group. Correspondingly, the expression patterns of the C2H2-ZF genes indicated that they function in different tissues and at different developmental stages. Additionally, quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 34 selected C2H2-ZFs are changed dramatically among the roots, stems, and leaves at different time points of a heat stress treatment, suggesting that the C2H2-ZFPs are extensively involved in the heat stress response but have potentially varying roles. These results form the basis for the further molecular and functional analysis of the C2H2-ZFPs, especially for those members that significantly varied under heat treatment, which may be targeted to improve the heat tolerance of tomato and other Solanaceae species.

Genome wide identification and expression analysis of pepper C2H2 zinc finger transcription factors in response to anthracnose pathogen Colletotrichum truncatum

“…Previous reports have shown that genes with no introns or shorter introns are inclined to be retained in plants and are rapidly activated in response to environmental challenges (Li and Liu 2019). Consequently, pepper ZFPs with shorter gene structure may have significant involvement in responding to biotic and abiotic stresses as has been demonstrated in other plant species (Hu et al 2019;Alam et al 2019;Yuan et al 2018). Interestingly, CanZF4 and CanZF71 with only one exon were also grouped with other genes in the same phylogenetic group with six to nine exons Fig.…”

“…Compared to other eukaryotic organisms, the plant C 2 H 2 ZFPs are characterized by long and diverse space between tandem zinc fingers and presence of a conserved QALGGH sequence in the ZF domain of the α-helix. C 2 H 2 -ZFP family has been comprehensively defined in several plant genomes including 179 in Arabidopsis thaliana (Englbrecht et al 2004), 189 in rice (Agrawal et al 2007), 122 in wheat (Faraji et al 2018), 124 in foxtail millet (Muthamilarasan et al 2014), 109 in poplar (Liu et al 2015) and 104 in tomato (Hu et al 2019). C 2 H 2 ZFPs exhibit extensive structural and functional variations including transcriptional regulation, RNA metabolism and protein-protein interactions.…”

OBV (obscure vein), a C2H2 zinc finger transcription factor, positively regulates chloroplast development and bundle sheath extension formation in tomato (Solanum lycopersicum) leaf veins

“…Functional analysis indicated that OBV encoded a C 2 H 2 L domain class transcription factor with a typical C-X2-C-X12-H-X3-H single ZF structure located in the N-terminal region of Solyc05g054030 . In tomato species, a total of 104 C 2 H 2 -ZFs have been identified 45 , most of which are associated with metal ion binding, DNA-binding transcription factor activity, the nucleus and regulation of transcription, and DNA templating. We found that Solyc05g054030 was related to shoot gravitropism.…”

A C2H2-Type Zinc-Finger Protein from Millettia pinnata, MpZFP1, Enhances Salt Tolerance in Transgenic Arabidopsis

“…The first C2H2-type ZFP gene discovered in plants was EPF1 , from Petunia [ 12 ]. EPF1-related proteins have been demonstrated to enhance tolerance to abiotic stresses in several plant species [ 17 , 18 , 19 , 20 ].…”

“…In the past two decades, many C2H2 ZFP genes have been identified and studied in model plants, such as Arabidopsis, rice ( Oryza sativa ), soybean ( Glycine max ), and tomato ( Solanum lycopersicum ) [ 17 , 18 , 20 , 21 , 22 ]. The overexpression of Arabidopsis C2H2 zinc finger protein STZ/ZAT10 enhanced tolerance to salinity, heat and osmotic stress in transgenic Arabidopsis [ 18 , 23 ].…”