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.

Figure 1.

Intron distribution within the basic and hinge regions of the bZIP domains of OsbZIP proteins. Intron distribution patterns (a–g) are depicted. An example of a sequence in the basic and hinge regions is shown at the top with arrows indicating the position of two introns (as observed in the majority of OsbZIP proteins), interrupted by black vertical lines in the sequence and the bars (representing the sequence in different intron patterns). The number of introns and the number of OsbZIP proteins having a particular pattern are also indicated. P0 and P2 indicate the splicing phases of the basic and hinge regions of the bZIP domains, where P0 and P2 refer to phase 0 and phase 2, respectively.

Figure 2.

Genomic distribution of OsbZIP genes on rice chromosomes. OsbZIP genes are numbered 1 to 89. Yellow ovals on the chromosomes (vertical bars) indicate the position of centromeres. Chromosome numbers are indicated at the top of each bar and the number in parentheses corresponds to the number of OsbZIP genes present on that chromosome. The OsbZIP genes present on duplicated chromosomal segments are connected by colored lines (one color per chromosome). The red and blue triangles indicate the upward and downward direction of transcription, respectively. The position of OsbZIP genes on TIGR rice chromosome pseudomolecules (release 5) is given in the Supplemental Table S2.

Figure 3.

Protein structure of representative OsbZIP proteins based on the position of the bZIP domain and the presence of additional conserved motifs outside the bZIP domain as identified by MEME. The bZIP domains are shown in blue, except the unusual bZIP domain, which is shown in pink. Different motifs are highlighted in different color boxes with numbers 1 to 25, where the same number refers to the same motif present in the different OsbZIP proteins. OsbZIP protein numbers having similar protein structure are given in front of each structure on the right side. The details of predicted conserved motifs are given in Supplemental Table S4.

Figure 4.

Amino acid analysis at the g, e, a, and d positions of the Leu zipper. A, Histogram of frequency of amino acids in the g, e, a, and d positions of the Leu zipper for the OsbZIP, AtbZIP, and HsbZIP proteins. B, Histogram of the frequency of Asn residue in the a position of the Leu zippers for all OsbZIP proteins.

Figure 5.

Histogram of the frequency of attractive or repulsive g↔e′ pairs per heptad for all OsbZIP proteins.

Figure 6.

Phylogenetic relationship among the OsbZIP proteins. The phylogenetic tree is based on the sequence alignments of the OsbZIP proteins. The unrooted tree was generated using ClustalX by the neighbor-joining method. Bootstrap values from 1,000 replicates are indicated at each node. OsbZIP proteins are grouped into 10 distinct clades (A–J).

Figure 7.

Expression profiles of OsbZIP genes differentially expressed during panicle and seed development. Expression profiles of nine up-regulated (A) and two down-regulated (B) OsbZIP genes in SAM or any stage of panicle development (P1-I–P1-III and P1–P6) as compared to vegetative reference tissues/organs (seedling, root, mature leaf, and Y leaf) and seed developmental stages (S1–S5) are presented. Expression profiles of nine up-regulated (C) and one down-regulated (D) OsbZIP genes in any stage of seed development (S1–S5) compared to vegetative reference tissues/organs (seedling, root, mature leaf, and Y leaf), SAM, and panicle developmental stages (P1-I–P6) are presented. The average log signal values of OsbZIP genes in various tissues/organs and developmental stages (mentioned at the top of each lane) are presented by cluster display. The color scale (representing log signal values) is shown at the bottom.

Figure 8.

Differential expression of OsbZIP genes under different light conditions based on microarray analysis from an earlier study (Jiao et al. 2005). A, Number of genes differentially expressed in various organs (mentioned below each bar) under white light. B, Number of differentially expressed genes in seedlings under different light conditions (mentioned below each bar; F, far-red; R, red; B, blue).

Figure 9.

Expression profiles of OsbZIP genes differentially expressed under abiotic stress conditions. Expression profiles of 26 significantly up-regulated (A) and 11 significantly down-regulated (B) OsbZIP genes as compared to the control seedlings. The average log signal values of OsbZIP genes under control and various stress conditions (mentioned at the top of each lane) are presented by cluster display (values are given in Supplemental Table S11). Only those genes that exhibited 2-fold or more differential expression with a P value ≤0.05 under any of the given abiotic stress conditions are shown. The color scale (representing log signal values) is shown at the bottom of each. C and D, Venn diagram of the number of differentially expressed OsbZIP genes under abiotic stress conditions. Number of up-regulated (C) and down-regulated (D) OsbZIP genes in any of the abiotic stress conditions as compared to control seedlings are given.