The WRKY Gene Family in Rice (Oryza sativa)

Abstract

WRKY genes encode transcription factors that are involved in the regulation of various biological processes. These zinc-finger proteins, especially those members mediating stress responses, are uniquely expanded in plants. To facilitate the study of the evolutionary history and functions of this supergene family, we performed an exhaustive search for WRKY genes using HMMER and a Hidden Markov Model that was specifically trained for rice. This work resulted in a comprehensive list of WRKY gene models in Oryza sativa L. ssp. indica and L. ssp. japonica. Mapping of these genes to individual chromosomes facilitated elimination of the redundant, leading to the identification of 98 WRKY genes in japonica and 102 in indica rice. These genes were further categorized according to the number and structure of their zinc-finger domains. Based on a phylogenetic tree of the conserved WRKY domains and the graphic display of WRKY loci on corresponding indica and japonica chromosomes, we identified possible WRKY gene duplications within, and losses between the two closely related rice subspecies. Also reviewed are the roles of WRKY genes in disease resistance and responses to salicylic acid and jasmonic acid, seed development and germination mediated by gibberellins, other developmental processes including senescence, and responses to abiotic stresses and abscisic acid in rice and other plants. The signaling pathways mediating WRKY gene expression are also discussed. Available online at www.blackwell-synergy.com/links/toc/jipb, www.jipb.net Plants, because of their inability to escape predation or environmental changes, have evolved strategies to tolerate and adapt to biotic and abiotic stresses. Biotic stresses, such as fungal, bacterial, and viral challenges, and abiotic stresses, such as drought, cold, wounding, and salinity, are sensed through a complex signal transduction network and result in physiological, biochemical, and gene expression changes (Kunkel and Brooks 2002;Singh et al. 2002; Mahalingam et al. 2003; Katagiri 2004). Families of transcription factors, central to this process, have uniquely expanded and evolved in plants to coordinate gene expression. The WRKY class of zinc-finger proteins, similar to the ethylene-responsive-element binding factors (ERF) (Gutterson and Reuber 2004), DNA binding one finger (Dof;Yanagisawa 2002Yanagisawa , 2004 and basic domain leucine zipper (bZIP;Siberil et al. 2001; Jakoby et al. 2002) families, is a family of proteins that contains many members that mediate plant stress responses (previously reviewed in Eulgem et al. 2000;Ulker and Somssich 2004). In the present review, we present the signature and domain of the WRKY genes, their distribution and evolution history, comprehensive analyses of rice WRKY family, and the regulation and functions of WRKY genes in rice and other plants. The WRKY Signature and DomainWRKY domains were initially defined by a nearly 60 amino acid long motif possessing the well-conserved amino acid signature WRKYGQK at their N-terminus and conta...

The Role of WRKY Transcription Factors in Plant Immunity

“…The rice genome contains more than 100 WRKY genes, often present in duplicated chromosomal regions, suggesting genome duplications as one of the mechanisms for the expansion of this family in this plant species (Ross et al, 2007;Ramamoorthy et al, 2008). The majority of these genes respond to (a)biotic stresses and various phytohormones (Ryu et al, 2006;Ramamoorthy et al, 2008).…”

“…The WRKY TF superfamily consists of 74 and 109 members in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), respectively (Eulgem and Somssich, 2007;Ross et al, 2007). Members of this family contain at least one conserved DNA-binding region, designated the WRKY domain, comprising the highly conserved WRKYGQK peptide sequence and a zinc finger motif (CX 4-7 CX 22-23 HXH/C).…”

Characterization of an Elicitor-Induced Rice WRKY Gene,OsWRKY71

“…[4][5][6] They have been investigated extensively for their possible involvement in defense responses against attack by pathogens, mainly in dicotyledonous plants. 7,8) The rice genome is predicted to contain over 100 WRKY (OsWRKY) genes.…”

Identification of a drought- and cold-stress inducibleWRKYgene in the cold-hardyCitrusrelativePoncirus trifoliata

“…A number of WRKY genes having these features have been identified based on sequence analyses in various plant species including Arabidopsis thaliana, rice (Oryza sativa), poplar (Populus spp. ), papaya (Carica papaya) and sorghum (Sorghum colar) (Eulgem et al 2000;Zhang and Wang 2005;Eulgem & Somssich 2007;Ross et al 2007;Pandey and Somssich 2009).…”