Genome-Wide Analysis of bZIP-Encoding Genes in Maize

Abstract

In plants, basic leucine zipper (bZIP) proteins regulate numerous biological processes such as seed maturation, flower and vascular development, stress signalling and pathogen defence. We have carried out a genome-wide identification and analysis of 125 bZIP genes that exist in the maize genome, encoding 170 distinct bZIP proteins. This family can be divided into 11 groups according to the phylogenetic relationship among the maize bZIP proteins and those in Arabidopsis and rice. Six kinds of intron patterns (a–f) within the basic and hinge regions are defined. The additional conserved motifs have been identified and present the group specificity. Detailed three-dimensional structure analysis has been done to display the sequence conservation and potential distribution of the bZIP domain. Further, we predict the DNA-binding pattern and the dimerization property on the basis of the characteristic features in the basic and hinge regions and the leucine zipper, respectively, which supports our classification greatly and helps to classify 26 distinct subfamilies. The chromosome distribution and the genetic analysis reveal that 58 ZmbZIP genes are located in the segmental duplicate regions in the maize genome, suggesting that the segment chromosomal duplications contribute greatly to the expansion of the maize bZIP family. Across the 60 different developmental stages of 11 organs, three apparent clusters formed represent three kinds of different expression patterns among the ZmbZIP gene family in maize development. A similar but slightly different expression pattern of bZIPs in two inbred lines displays that 22 detected ZmbZIP genes might be involved in drought stress. Thirteen pairs and 143 pairs of ZmbZIP genes show strongly negative and positive correlations in the four distinct fungal infections, respectively, based on the expression profile and Pearson's correlation coefficient analysis.

Zygotic Genome Activation Occurs Shortly after Fertilization in Maize

“…The first four classes are related to plastid development (Zhou et al, 1995;Ouyang et al, 2011;Kleine, 2012;Wei et al, 2012). This finding suggests that a tightly controlled regulatory network controls plastid development during the first steps in the plant life cycle.…”

Genome-Wide Identification and Analysis of bZIP Family and their Expression in Response to Multiple Abiotic Stresses in Malus domestica

“…The bZIP genes, encoding a big family of transcription factors, are ubiquitous present in eukaryote, from unicellular saccharomycetes [37] to vascular plants. The structure, evolution and function of bZIP genes have been thoroughly studied in Arabidopsis [7], rice [8], maize [31], cucumber [3], soybean [10], sorghum [9] and Brachypodium distachyon [24]. Most of the studies were focused on Gramineae and Cucurbitaceae, while little is known about the bZIP family in Rosaceae.…”

“…When function as transcription factors by binding to DNA, leucine zipper region of bZIPs should be dimerized to keep the stability of binding. Based on analysis of the leucine zipper dimerization specificity of bZIPs from H. sapiens [5], Arabidopsis [40], rice [8] and maize [31], the same structural rules of dimerization specificity of M.bZIP proteins were investigated. Base on the standard nomenclature for the seven unique amino acid positions (a, d, e and g) to arrange in the leucine zipper region, 116 M.bZIPs can be categorized into 29 subfamilies (BZ1-BZ29).…”

“…Following this criteria, two to nine heptads were identified in different M.bZIPs (Table S5). Stability and specificity of leucine zipper dimmer are closely related to the amino acids present at the position a, d, e and g, since they are near the interface of leucine zipper [31]. Amino acids at the position a and d are typically hydrophobic, forming a hydrophobic core is essential for interaction between two monomers.…”

“…Attractive pairs and presence of Asn in position a contribute to homo285 dimerization, while repulsive and incomplete pairs, and charged residues in position a may tend to hetero-dimerization [24,31]. According to these principles, total 116 M.bZIPs were classified into 29 sub-families (Table S5).…”