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

Xingguo Zhang,Li Xu,Yi Zhang,Lili Zhu,Na Li,Xin Hu,Yu Pan

doi:10.7717/peerj.7929

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.

Highlights

The zinc finger proteins (ZFPs) are one of the largest protein families in plants
The tomato genome (The Tomato Genome, 2012) and protein sequences were used to construct a local protein database using Geneious v4.8.5 software, which was BLASTP searched using the sequences of the A. thaliana C2H2-ZFPs as queries, with an E-value cut-off ≤ 1 × 10−20
We found that genes in the same group had the highly similar intron/exon arrangements in the Neighbor Joining (NJ) phylogenetic tree (Fig. 3), indicating that the gene structure patterns were consistent with the NJ phylogenetic analysis

Summary

Introduction

The zinc finger proteins (ZFPs) are one of the largest protein families in plants. These proteins harbor a highly conserved domain, in which a zinc ion is surrounded by cysteine (Cys) and/or histidine (His) residues to stabilize their three-dimensional structure, comprising a two-stranded antiparallel beta sheets and a helix (Liu et al, 2015). C3H (Nup 475), C3HC4 (RING finger), C4 (GATA-1), C4HC3 (Requium), C6 (GAL4), and C8 (Steroid-thyroid receptor) (Berg & Shi, 1996; Liu et al, 2015; Michael & Chrisopher, 2003). The members of these classes play crucial roles in plant growth and development, as well as in signal transduction and environmental stress responses (Takatsuji, 1998; Stege et al, 2002; Le Gall et al, 2015; Yin et al, 2017)

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Discussion

Conclusion