Genomic Survey and Gene Expression Analysis of the Basic Leucine Zipper Transcription Factor Family in Rice

Abstract

The basic leucine (Leu) zipper (bZIP) proteins compose a family of transcriptional regulators present exclusively in eukaryotes. The bZIP proteins characteristically harbor a bZIP domain composed of two structural features: a DNA-binding basic region and the Leu zipper dimerization region. They have been shown to regulate diverse plant-specific phenomena, including seed maturation and germination, floral induction and development, and photomorphogenesis, and are also involved in stress and hormone signaling. We have identified 89 bZIP transcription factor-encoding genes in the rice (Oryza sativa) genome. Their chromosomal distribution and sequence analyses suggest that the bZIP transcription factor family has evolved via gene duplication. The phylogenetic relationship among rice bZIP domains as well as with bZIP domains from other plant bZIP factors suggests that homologous bZIP domains exist in plants. Similar intron/exon structural patterns were observed in the basic and hinge regions of their bZIP domains. Detailed sequence analysis has been done to identify additional conserved motifs outside the bZIP domain and to predict their DNA-binding site specificity as well as dimerization properties, which has helped classify them into different groups and subfamilies, respectively. Expression of bZIP transcription factor-encoding genes has been analyzed by full-length cDNA and expressed sequence tag-based expression profiling. This expression profiling was complemented by microarray analysis. The results indicate specific or coexpression patterns of rice bZIP transcription factors starting from floral transition to various stages of panicle and seed development. bZIP transcription factor-encoding genes in rice also displayed differential expression patterns in rice seedlings in response to abiotic stress and light irradiation. An effort has been made to link the structure and expression pattern of bZIP transcription factor-encoding genes in rice to their function, based on the information obtained from our analyses and earlier known results. This information will be important for functional characterization of bZIP transcription factors in rice.

Defining Core Metabolic and Transcriptomic Responses to Oxygen Availability in Rice Embryos and Young Seedlings

“…6B, no. 46; Supplemental Table S9) has previously been identified to encode a heat shock transcription factor (Yamanouchi et al, 2002), and another (LOC_ Os03g26210.1) increased under dehydration stress (Nijhawan et al, 2008). This group also contains a number of myb-type transcription factors previously associated with stress responses (Yanhui et al, 2006).…”

Constitutive Activation of Transcription Factor OsbZIP46 Improves Drought Tolerance in Rice

“…We identified the full-length cDNA of OsbZIP46, designated according to Nijhawan et al (2008), in a cDNA library of Minghui 63 (Chu et al, 2003;Zhang et al, 2005;Supplemental Fig. S1).…”

“…Rice plants have 89 putative bZIP transcription factor genes (Nijhawan et al, 2008). Several members have been studied for their functions potentially related to stress responses, such as LIP19 (Shimizu et al, 2005), OsBZ8 (Nakagawa et al, 1996;Mukherjee et al, 2006), and RF2a and RF2b (Dai et al, 2004(Dai et al, , 2008.…”

“…Among the transcription factors, members of the bZIP family, which contain a basic region and a Leu zipper domain, have been identified for their function in the ABA-dependent pathway by recognizing ABA-responsive elements (ABREs) containing an ACGT core motif. As a big transcription factor family, quite a few bZIP transcription factors have been well characterized functionally with diverse roles in many aspects, including pathogen defense, light signaling, seed maturation, flower development, and, especially, abiotic stress responses and hormone signal transduction (Uno et al, 2000;Jakoby et al, 2002;Nijhawan et al, 2008). Among the studies of the bZIP family, a noteworthy aspect is that the function of the third subfamily (also known as the AREB/ABF/ ABI5 subfamily) has been well elucidated because of the prominent roles of this subfamily in the ABA signaling pathway.…”

A Drought-Inducible Transcription Factor Delays Reproductive Timing in Rice

“…One such class of TFs consists of a subgroup of bZIP proteins, which contain a basic region for DNA binding and a Leu zipper motif for dimerization. The DNA binding region preferentially interacts with ABA-responsive elements (ABREs), which are predominantly located in the promoter regions of ABAinducible genes (Jakoby et al, 2002;Nijhawan et al, 2008). A great deal of genetic evidence shows that these ABRE-associated bZIP TFs are involved in drought tolerance response (Kang et al, 2002;Oh et al, 2005;Xiang et al, 2008;Lu et al, 2009;Hossain et al, 2010aHossain et al, , 2010bTang et al, 2012).…”