Genome-wide identification of C2H2 zinc-finger gene family in rice and their phylogeny and expression analysis

Abstract

Transcription factors regulate gene expression in response to various external and internal cues by activating or suppressing downstream genes in a pathway. In this study, we provide a complete overview of the genes encoding C(2)H(2) zinc-finger transcription factors in rice, describing the gene structure, gene expression, genome localization, and phylogenetic relationship of each member. The genome of Oryza sativa codes for 189 C(2)H(2) zinc-finger transcription factors, which possess two main types of zinc-fingers (named C and Q). The Q-type zinc fingers contain a conserved motif, QALGGH, and are plant specific, whereas C type zinc fingers are found in other organisms as well. A genome-wide microarray based gene expression analysis involving 14 stages of vegetative and reproductive development along with 3 stress conditions has revealed that C(2)H(2) gene family in indica rice could be involved during all the stages of reproductive development from panicle initiation till seed maturation. A total of 39 genes are up-regulated more than 2-fold, in comparison to vegetative stages, during reproductive development of rice, out of which 18 are specific to panicle development and 12 genes are seed-specific. Twenty-six genes have been found to be up-regulated during three abiotic stresses and of these, 14 genes express specifically during the stress conditions analyzed while 12 are also up-regulated during reproductive development, suggesting that some components of the stress response pathways are also involved in reproduction.

The REIL1 and REIL2 Proteins ofArabidopsis thalianaAre Required for Leaf Growth in the Cold

“…The eudicot model plant Arabidopsis thaliana, for example, has 176 zinc finger proteins (Englbrecht et al, 2004;Ciftci-Yilmaz and Mittler, 2008). A family of 189 zinc finger proteins is encoded by the genome of the monocot model Oryza sativa (Agarwal et al, 2007). Most of the members of these large protein families are plant-specific transcriptional regulators.…”

“…Most of the members of these large protein families are plant-specific transcriptional regulators. Plant zinc finger proteins contain one or more typical C2H2-type zinc finger domains but may also have variations of this motif (Englbrecht et al, 2004;Agarwal et al, 2007;Ciftci-Yilmaz and Mittler, 2008). Only 32 proteins of A. thaliana contain four zinc finger domains.…”

RID1 , encoding a Cys2/His2-type zinc finger transcription factor, acts as a master switch from vegetative to floral development in rice

“…The id1 mutant has prolonged vegetative growth and retains vegetative features in the inflorescence (19). ID1 encodes a Cys-2/His-2 zinc-finger protein (19), one of the largest classes of transcription factor families in eukaryotes, playing roles in diverse biological processes (20,21). Expression of ID1 is limited to developing leaves, indicating a noncell autonomous effect on the vegetative-to-reproductive state of the apical meristem (19,22,23).…”

Cross-tolerance to Thermal Stresses and its Application to the Development of Cold Tolerant Rice

“…However, the transformants with several introduced TF genes might represent such off-target effects as dwarfism and retarded growth, when expression of the TF was enhanced under normal conditions (Ito et al 2006, Wu et al 2009, Xu et al 2011). The expression of most TFs listed in Table 1 is enhanced by stress conditions (Sakuma et al 2002, Agarwal et al 2007, Saad et al 2010, Takasaki et al 2010. TFs sometimes respond to the presence of ROS such as H2O2 via protein kinases, through Ca 2+ as a second messenger, a mechanism common to plant responses to several abiotic stresses (Wang et al 2003).…”