Genome-wide identification and expression analysis of the bZIP transcription factor family genes in response to abiotic stress in Nicotiana tabacum L

Abstract

Background: The basic leucine zipper (bZIP) transcription factor (TF) is one of the largest families of transcription factors (TFs). It is widely distributed and highly conserved in animals, plants, and microorganisms. Previous studies have shown that the bZIP TF family is involved in plant growth, development, and stress responses. The bZIP family has been studied in many plants; however, there is little research on the bZIP gene family in tobacco.

Results: In this study, 77 bZIPs were identified in tobacco and named NtbZIP01 through to NtbZIP77. These 77 genes were then divided into eleven subfamilies according to their homology with Arabidopsis thaliana. NtbZIPs were unevenly distributed across twenty-two tobacco chromosomes, and we found sixteen pairs of segmental duplication. We further studied the collinearity between these genes and related genes of six other species. Quantitative real-time polymerase chain reaction analysis identified that expression patterns of bZIPs differed, including in different organs and under various abiotic stresses. NtbZIP49 might be important in the development of flowers and fruits; NtbZIP18 might be an important regulator in abiotic stress.

Conclusions: In this study, the structures and functions of the bZIP family in tobacco were systematically explored. Many bZIPs may play vital roles in the regulation of organ development, growth, and responses to abiotic stresses. This research has great significance for the functional characterisation of the tobacco bZIP family and our understanding of the bZIP family in higher plants.

Keywords: Abiotic stress; Gene expression patterns; Nicotiana tabacum L.; bZIP family.

Fig. 1

Unrooted phylogenetic tree showing relationships between the bZIP domains of Nicotiana tabacum L.and Arabidopsis thaliana. The phylogenetic tree was derived using the neighbour-joining method in MEGA X. The tree shows the 11 phylogenetic subfamilies (red). bZIP proteins from Arabidopsis are indicated by the prefix ‘At’. bZIP: basic leucine zipper; MEGA: Molecular Evolutionary Genetics Analysis

Fig. 2

Phylogenetic relationships, gene structure analysis, and motif distributions of Nicotiana tabacum L. bZIPs. bZIP: basic leucine zipper. a Phylogenetic tree constructed by the neighbour-joining method, with 1000 replicates on each node. b Amino acid motifs in the bZIP proteins (1–10) are represented by coloured boxes. Black lines indicate relative protein lengths. c Exons and introns are indicated by green rectangles, and grey lines, respectively

Fig. 3

Schematic representation of the chromosomal distribution of the Nicotiana tabacum L. bZIPs. Vertical bars represent the tobacco chromosomes. Chromosome number is indicated to the left of each chromosome (yellow). bZIP: basic leucine zipper

Fig. 4

Schematic representation of the chromosomal distribution and interchromosomal relationships of Nicotiana tabacum L. bZIPs. Coloured lines indicate all synteny blocks in the N. tabacum genome; red lines indicate duplicated bZIP gene pairs. Chromosome number is indicated at the bottom of each chromosome. bZIP: basic leucine zipper

Fig. 5

Synteny analyses of the bZIPs between Nicotiana tabacum and 7 representative plant species (Arabidopsis thaliana, Oryza sativa, Fagopyrum tataricum, Solanum lycopersicum, Hordeum vulgare, Vitis vinifera and Solanum tuberosum). Grey lines on the background indicate the collinear blocks in N. tabacum and other plant genomes; red lines highlight the syntenic N. tabacum bZIP gene pairs. bZIP: basic leucine zipper. Outer panel: An unrooted phylogenetic tree constructed using Geneious R11 with the neighbour-joining method. Inner panel: Distribution of the conserved motifs in bZIP proteins. The differently coloured boxes represent different motifs and their positions in each bZIP protein sequence. The sequence information for each motif is provided in Additional file 2: Table S2

Fig. 6

Tissue-specific gene expression of 11 Nicotiana tabacum L. bZIPs and the correlation between their expression patterns. bZIP: basic leucine zipper; qRT-PCR: Real-time quantitative PCR. a Expression patterns of 11 Nicotiana tabacum L. bZIPs in the calyx, petal, anther, stigma, leaf, stem, fruit, and root organs, as examined by qRT-PCR. Error bars represent standard error. Lowercase letters above bars indicate a significant difference (P < 0.05, least significant difference test) among the treatments. b Positive number: positively correlated; negative number: negatively correlated. Red numbers indicate a significant correlation at the 0.05 level

Fig. 7

Expression of 11 Nicotiana tabacum L. bZIPs in plants subjected to abiotic stresses (strong UV radiation, flooding, PEG, NaCl, and hot and cold treatments) at the seedling stage. bZIP: basic leucine zipper; qRT-PCR: Real-time quantitative PCR. a Expression patterns of 11 Nicotiana tabacum L. bZIPs in leaf, root, and stem organs were examined by qRT-PCR. Error bars represent standard error. Lowercase letters above bars indicate a significant difference (P < 0.05, LSD) among the treatments. bZIP: basic leucine zipper; qRT-PCR: Real-time quantitative PCR. b Positive number: positively correlated; negative number: negatively correlated. Red numbers indicate a significant correlation at the 0.05 level