Genome-Wide Identification and Expression Analysis of the Basic Leucine Zipper (bZIP) Transcription Factor Gene Family in Fusarium graminearum

Abstract

The basic leucine zipper (bZIP) is a widely found transcription factor family that plays regulatory roles in a variety of cellular processes including cell growth and development and various stress responses. However, the bZIP gene family has not been well studied at a genome-wide scale in Fusarium graminearum (Fg), a potent pathogen of cereal grains. In the present study, we conducted a genome-wide identification, characterization, and expression profiling of 22 F. graminearum bZIP (FgbZIP) genes at different developmental stages and under various abiotic stresses. All identified FgbZIPs were categorized into nine groups based on their sequence similarity and phylogenetic tree analysis. Furthermore, the gene structure analysis, conserved motif analysis, chromosomal localization, protein network studies, and synteny analysis were performed. The symmetry of the exon and intron varied with the phylogenetic groups. The post-translational modifications (PTMs) analysis also predicted several phosphorylation sites in FgbZIPs, indicating their functional diversity in cellular processes. The evolutionary study identified many orthogroups among eight species and also predicted several gene duplication events in F. graminearum. The protein modeling indicated the presence of a higher number of α-helices and random coils in their structures. The expression patterns of FgbZIP genes showed that 5 FgbZIP genes, including FgbZIP_1.1, FgbZIP_1.3, FgbZIP_2.6 FgbZIP_3.1 and FgbZIP_4.3, had high expression at different growth and conidiogenesis stages. Similarly, eight genes including FgbZIP_1.1, FgbZIP_1.6, FgbZIP_2.3, FgbZIP_2.4, FgbZIP_4.1, FgbZIP_4.2, FgbZIP_4.3 and FgbZIP_4.6 demonstrated their putative role in response to various abiotic stresses. In summary, these results provided basic information regarding FgbZIPs which are helpful for further functional analysis.

Keywords: Fusarium graminearum; abiotic stress; bZIP; expression analysis; phylogenetic.

Figure 1

Multiple Sequence alignment of FgbZIP amino acids performed by MAFFT algorithm using UGENE. The representative model of both basic (yellow strip) and leucine zipper (blue strip) region are shown above by highlighting and labelling. Green, red and blue colored amino acids indicate conserved amino acid residues of bZIP gene family. While contrast colors in the conserved region depicts the position replaced by other less conserved amino acids.

Figure 2

Phylogenetic tree constructed using 135 full-length bZIP protein sequences. The phylogenetic tree was constructed in MEGAX using maximum likelihood method after aligning with the ClustalW program and the bootstrap iterations value was 1000 to generate tree. The proteins are clustered into nine clades (A–I) indicated by colored branches. The FgbZIPs are denoted by pink circles while. Ashbya gossypii, Aspergillus nidulans, Neurospora crassa, S. cerevisiae, Schizosaccharomyces pombe, S. sclerotiorum and Ustilago maydis are indicated with orange, blue, green, yellow, silver, red and dark green colored circles respectively.

Figure 3

Evolutionary study of bZIP in Fungal species. (A); bZIP Based phylogenetic tree of species Schizo saccharomyces pombe (Spb), Ustilago maydis (Unm), Ashbya gossypii (Agb), S. cerevisiae (Scb), Fusarium graminearum (Fgb), N. crassa (Ncb), A. nidulans (Anb), Sclerotinia sclerotiorum (SLs), (B); Orthologs summary, (C); Gene duplication events among fungal species, (D); orthogroups duplication events in all 135 genes.

Figure 4

Gene structure of F. graminearum bZIP genes it displays exons, intron and intron phase on a bp scale. The phylogenetic tree on the left was constructed based on the full-length sequences of the FgbZIP proteins. While the alphabets A-F shows groups.

Figure 5

Conserved motif analysis of bZIP genes derived using Pfam figure showing conserved motifs highlighted in different colors, where bZIP is prominent in each gene.

Figure 6

String network analysis of FgbZIP genes.

Figure 7

Relative expression pattern of FgbZIP genes under different stages of development. Relative expression values of RT-qPCR results were transformed by log2. Light and dark colored boxes reveal lower and higher expression levels, respectively according to the scale. The alphabets A–D on the right depicts grouping based on the expression of genes.

Figure 8

Expression profiles of FgbZIP genes response to abiotic stress. Relative expression values of RT_qPCR results were transformed by log2. Fold changes in gene expression are shown in color according to the scale. NaCl: sodium chloride, Sorb: Sorbitol, SDS: sodium dodecyl sulfate, H₂O₂: hydrogen peroxide, Low Temp: low temperature (4 °C), High Temp: high temperature (37 °C).

Figure 9

(A) Synteny analysis and chromosome localizations of F. graminearum (FgbZIP) genes (Paralogs). Block regions with orange color represent Fg chromosomes and genes indicated on a scale of bp paralogs colors and line pattern is according to phylogenetic trees clades displayed during gene structure analysis. (B) Synteny analysis (Orthologs) between F. graminearum whose chromosomes are indicated with blue color block and N. crassa whose chromosomes are indicated with green blocks, Supplementary File S5.