Genome-wide identification and analysis of the TIFY gene family in grape.

Yucheng Zhang,Stacy D Singer,Zhangjun Fei,Min Gao,Hua Wang,Xiping Wang

doi:10.1371/journal.pone.0044465

Abstract

BackgroundThe TIFY gene family constitutes a plant-specific group of genes with a broad range of functions. This family encodes four subfamilies of proteins, including ZML, TIFY, PPD and JASMONATE ZIM-Domain (JAZ) proteins. JAZ proteins are targets of the SCFCOI1 complex, and function as negative regulators in the JA signaling pathway. Recently, it has been reported in both Arabidopsis and rice that TIFY genes, and especially JAZ genes, may be involved in plant defense against insect feeding, wounding, pathogens and abiotic stresses. Nonetheless, knowledge concerning the specific expression patterns and evolutionary history of plant TIFY family members is limited, especially in a woody species such as grape.Methodology/Principal FindingsA total of two TIFY, four ZML, two PPD and 11 JAZ genes were identified in the Vitis vinifera genome. Phylogenetic analysis of TIFY protein sequences from grape, Arabidopsis and rice indicated that the grape TIFY proteins are more closely related to those of Arabidopsis than those of rice. Both segmental and tandem duplication events have been major contributors to the expansion of the grape TIFY family. In addition, synteny analysis between grape and Arabidopsis demonstrated that homologues of several grape TIFY genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of lineages that led to grape and Arabidopsis. Analyses of microarray and quantitative real-time RT-PCR expression data revealed that grape TIFY genes are not a major player in the defense against biotrophic pathogens or viruses. However, many of these genes were responsive to JA and ABA, but not SA or ET.ConclusionThe genome-wide identification, evolutionary and expression analyses of grape TIFY genes should facilitate further research of this gene family and provide new insights regarding their evolutionary history and regulatory control.

Highlights

TIFY proteins comprise a plant-specific family of putative transcription factors that are increasingly believed to play an important role in stress response
Among the 13 grape TIFY proteins that contained a Jas motif, two lacked the conserved PY motif at their C-termini, which is characteristic of PPD proteins [3], and included a PPD domain, which indicates that they are PPD proteins
In the present study we identified two TIFY, four ZML, two PPD, and 11 JASMONATE ZIM-Domain (JAZ) genes in the V. vinifera genome

Summary

Introduction

TIFY proteins comprise a plant-specific family of putative transcription factors that are increasingly believed to play an important role in stress response This family owes their name to a conserved motif (TIF[F/Y]XG) located within an approximately 36 amino acid long TIFY domain and can be divided into four groups based on both phylogenetic and structural analyses [1,2]. While all TIFY proteins bear a TIFY domain, those in the ZML subfamily, including ZIM (Zinc-finger expressed in Inflorescence Meristem) and ZIM-like (ZML) proteins, contain both a C2C2-GATA zinc-finger DNA-binding domain and a CCT domain (CONSTANS, CO-like, TOC1). Proteins from both PEAPOD (PPD) and JAZ subfamilies lack GATA and CCT domains [3]. Knowledge concerning the specific expression patterns and evolutionary history of plant TIFY family members is limited, especially in a woody species such as grape

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