Genome-Wide Analysis of the AP2/ERF Gene Family in Physic Nut and Overexpression of the JcERF011 Gene in Rice Increased Its Sensitivity to Salinity Stress.

Yuehui Tang,Huawu Jiang,Guojiang Wu,Pingzhi Wu,Yali Guo,Yaping Chen,Shanshan Qin,Meiru Li,Yanbo Chen

doi:10.1371/journal.pone.0150879

Abstract

The AP2/ERF transcription factors play crucial roles in plant growth, development and responses to biotic and abiotic stresses. A total of 119 AP2/ERF genes (JcAP2/ERFs) have been identified in the physic nut genome; they include 16 AP2, 4 RAV, 1 Soloist, and 98 ERF genes. Phylogenetic analysis indicated that physic nut AP2 genes could be divided into 3 subgroups, while ERF genes could be classed into 11 groups or 43 subgroups. The AP2/ERF genes are non-randomly distributed across the 11 linkage groups of the physic nut genome and retain many duplicates which arose from ancient duplication events. The expression patterns of several JcAP2/ERF duplicates in the physic nut showed differences among four tissues (root, stem, leaf, and seed), and 38 JcAP2/ERF genes responded to at least one abiotic stressor (drought, salinity, phosphate starvation, and nitrogen starvation) in leaves and/or roots according to analysis of digital gene expression tag data. The expression of JcERF011 was downregulated by salinity stress in physic nut roots. Overexpression of the JcERF011 gene in rice plants increased its sensitivity to salinity stress. The increased expression levels of several salt tolerance-related genes were impaired in the JcERF011-overexpressing plants under salinity stress.

Highlights

The APETALA2/ethylene response factor (AP2/ERF) superfamily of transcription factors is defined by the AP2/ERF domain, which consists of about 60 to 70 amino acids and is involved in DNA binding [1,2,3]
Sequences of AP2/ERF domain-containing proteins from Arabidopsis were downloaded from the Arabidopsis genome sequence, TAIR 9.0 release, while sequences for rice, castor bean, Chlamydomonas reinhardtii, and Physcomitrella patens were downloaded from Phytozome and sequences for grapevine were downloaded from Licausi et al [9]
Fifteen of these genes were assigned to the AP2 family due to their tandemly repeated double AP2/ERF domain

Summary

Introduction

The APETALA2/ethylene response factor (AP2/ERF) superfamily of transcription factors is defined by the AP2/ERF domain, which consists of about 60 to 70 amino acids and is involved in DNA binding [1,2,3]. On the basis of the protein structure and sequence similarity of the AP2/ERF domains, the AP2/ERF superfamily has been divided into 4 families: AP2, ERF, RAV, and Soloist [4, 5]. The AP2 family proteins contain two repeated AP2/ERF domains, the ERF and Soloist family proteins contain a single AP2/ERF domain, and the RAV family. AP2/ERF Genes in the Physic Nut Genome

Methods

Results

Discussion

Conclusion