Abstract
BackgroundAmong 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, ZjbZIPs 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.ResultsAt 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 ZjbZIPs, which would be beneficial to increase the protein production and also indicated that ZjbZIPs 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 ZjbZIPs 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.ConclusionsThe 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.
Highlights
Among several Transcription factors (TFs) families unique to eukaryotes, the basic leucine zipper family is one of the most important
The ORF length of the ZjbZIPs ranged from 384 bp (ZjbZIP44) to 2205 bp (ZjbZIP11), and they encoded proteins ranging from 127 (ZjbZIP44) to 749 (ZjbZIP11) amino acids in length, with predicted pIs ranging from 4.65 (ZjbZIP40) to 9.96 (ZjbZIP44) (Table 1) and predicted molecular weights (MWs) of 14.67–82.15 kDa
Relative Synonymous Codon Usage (RSCU) analyses will help us to understand the patterns in ZjbZIPs, and the RSCU values greater than 1.5 was defined as high-frequency codons [31]
Summary
Among several TF families unique to eukaryotes, the basic leucine zipper (bZIP) family is one of the most important. Members of the bZIP family are involved in the regulation of plant resistance under biotic and abiotic stresses [7,8,9], and play some important roles during plant growth and development processes, such as hormone signal transduction [10], energy metabolism [11], seedling development [12] and flowering [13]. BZIPs can be combined with cis- acting elements such as G-box (CACGTG), A-box (TACGTA) and abscisic acid (ABA)responsive elements (ABRE) (CCACGTGG) to regulate the expression of downstream genes. In Arabidopsis, ABF1, ABF2, ABF3 and ABF4 could bind to the cis-acting element ABRE, and regulate many downstream salt and drought tolerances through the interaction between ABRE and bZIP proteins [14]. AtbZIPs regulated the signal transduction of ABA-related pathways, thereby affecting seed germination and maturity [12]
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