Genome-wide analysis of the bZIP gene family in Chinese jujube (Ziziphus jujuba Mill.)

Abstract

Background Among several TF families unique to eukaryotes, the basic leucine zipper (bZIP) family is one of the most important. Chinese jujube ( Ziziphus jujuba Mill.) is a popular fruit tree species in Asia, and its fruits are rich in sugar, vitamin C and so on. Analysis of the bZIP gene family of jujube has not yet been reported. In this study, ZjbZIP s were identified firstly, their expression patterns were further studied in different tissues and in response to various abiotic and phytoplasma stresses, and their protein-protein interactions were also analyzed. Results At the whole genome level, 45 ZjbZIPs were identified and classified into 14 classes. The members of each class of bZIP subfamily contain a specific conserved domain in addition to the core bZIP conserved domain, which may be related to its biological function. Relative Synonymous Codon Usage (RSCU) analysis displayed low values of NTA and NCG codons in ZjbZIP s, which would be beneficial to increase the protein production and also indicated that ZjbZIP s were at a relative high methylation level. The paralogous and orthologous events occurred during the evolutionary process of ZjbZIPs . Thirty-four ZjbZIPs were mapped to but not evenly distributed among 10 pseudo- chromosomes. 30 of ZjbZIP genes showed diverse tissue-specific expression in jujube and wild jujube trees, indicating that these genes may have multiple functions. Some ZjbZIP genes were specifically analyzed and found to play important roles in the early stage of fruit development. Moreover, some ZjbZIP s that respond to phytoplasma invasion and abiotic stress environmental conditions, such as salt and low temperature, were found. Based on homology comparisons, prediction analysis and yeast two-hybrid, a protein interaction network including 42 ZjbZIPs was constructed. Conclusions The bioinformatics analyses of 45 ZjbZIPs were implemented systematically, and their expression profiles in jujube and wild jujube showed that many genes might play crucial roles during fruit ripening and in the response to phytoplasma and abiotic stresses. The protein interaction networks among ZjbZIPs could provide useful information for further functional studies.

Genome-wide characterization of bZIP gene family identifies potential members involved in flavonoids biosynthesis in Ginkgo biloba L.

“…Plants inhibit anthocyanin biosynthesis by degrading HY5 at high temperature 35 .

Figure 7 Protein–protein interaction network for GbbZIPs was analyzed by the STRING website ( http://string-db.org/ ) using the full-length protein sequence 16 , 36 . Empty nodes indicate proteins of unknown 3D structure.

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“…To bind DNA, two subunits adhere via interaction between the hydrophobic sides of their helices, which creates a superimposing coiled-coil structure 15 . ACGT is the core sequence recognized by bZIP TF, and the corresponding cis-acting elements are A-box, G-box, and C-box 14 , 16 .…”

Genome-wide identification and characterization of bZIP transcription factors and their expression profile under abiotic stresses in Chinese pear (Pyrus bretschneideri)

“…SlbZIP38 gene identified in tomato is a response to salt stress [71]. ZjbZIPs play roles in development under abiotic and biotic stresses [5]. 10 TGA family genes in Arabidopsis play important roles in the SA defense signaling pathway and necrotizing pathogens [5,72].…”

“…ZjbZIPs play roles in development under abiotic and biotic stresses [5]. 10 TGA family genes in Arabidopsis play important roles in the SA defense signaling pathway and necrotizing pathogens [5,72]. Plants improve their biotic and abiotic response after exogenous application of gibberellin, ethylene, SA, and ABA [73].…”

“…The length of the domain is 60-80 amino acids containing two regions with various functions; the basic region is highly conserved and consists of 16 amino acid residues with specific DNA binding (N-× 7-R/K-× 9) [4]. On the other hand, the leucine zipper is less conserved and composed of several helical structures, which are responsible for dimerization stability and specificity (homo/heterodimerization) [5].…”