Identification, expression, alternative splicing and functional analysis of pepper WRKY gene family in response to biotic and abiotic stresses.

Jingyuan Zheng,Xuexiao Zou,Xuefeng Li,Feng Liu,Yanqing Ma,Bozhi Yang,Xiongze Dai,Chunhui Zhu,Keqiang Wu

doi:10.1371/journal.pone.0219775

Abstract

WRKY proteins are a large group of plant transcription factors that are involved in various biological processes, including biotic and abiotic stress responses, hormone response, plant development, and metabolism. WRKY proteins have been identified in several plants, but only a few have been identified in Capsicum annuum. Here, we identified a total of 62 WRKY genes in the latest pepper genome. These genes were classified into three groups (Groups 1–3) based on the structural features of their proteins. The structures of the encoded proteins, evolution, and expression under normal growth conditions were analyzed and 35 putative miRNA target sites were predicted in 20 CaWRKY genes. Moreover, the response to cold or CMV treatments of selected WRKY genes were examined to validate the roles under stresses. And alternative splicing (AS) events of some CaWRKYs were also identified under CMV infection. Promoter analysis confirmed that CaWRKY genes are involved in growth, development, and biotic or abiotic stress responses in hot pepper. The comprehensive analysis provides fundamental information for better understanding of the signaling pathways involved in the WRKY-mediated regulation of developmental processes, as well as biotic and abiotic stress responses.

Highlights

WRKY transcription factors constitute one of the largest families of regulatory proteins in plants
To identify WRKY proteins encoded in the hot pepper genome, publicly available genome sequences of ZUNLA-1 were searched with the BLASTP, based on HMM
We identified a total of 62 hot pepper WRKY transcription factors and analyzed their phylogenetic relationships and conserved motifs

Summary

Introduction

WRKY transcription factors constitute one of the largest families of regulatory proteins in plants. Proteins in this family contain at least one or two highly conserved domains of ~60 amino acids, which are characterized by the hallmark heptapeptide WRKYGQK, followed by a C2H2 or C2HC zinc-finger motif [1, 2]. The WRKY domain facilitates binding to the W-box in the promoter of a target gene to modulate transcription [3]. As deduced from nuclear magnetic resonance (NMR) analysis of a WRKY domain of AtWRKY4, the conserved WRKYGQK sequence is directly involved in DNA binding [4]. WRKY proteins can be divided into three distinct groups based on the number of WRKY domains and certain features of the zinc-.

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