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Article

In-Depth Characterization of bZIP Genes in the Context of Endoplasmic Reticulum (ER) Stress in Brassica campestris ssp. chinensis

by
Aliya Ayaz
1,
Abdul Jalal
2,
Xiaoli Zhang
1,
Khalid Ali Khan
3,
Chunmei Hu
1,*,
Ying Li
1,* and
Xilin Hou
1
1
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
2
Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
3
Applied College, Center of Bee Research and Its Products (CBRP), Unit of Bee Research and Honey Production, and Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 61413, Saudi Arabia
*
Authors to whom correspondence should be addressed.
Plants 2024, 13(8), 1160; https://doi.org/10.3390/plants13081160
Submission received: 26 March 2024 / Revised: 13 April 2024 / Accepted: 16 April 2024 / Published: 22 April 2024
(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)
Browse Figures
Versions Notes

Abstract

:
Numerous studies have been conducted to investigate the genomic characterization of bZIP genes and their involvement in the cellular response to endoplasmic reticulum (ER) stress. These studies have provided valuable insights into the coordinated cellular response to ER stress, which is mediated by bZIP transcription factors (TFs). However, a comprehensive and systematic investigations regarding the role of bZIP genes and their involvement in ER stress response in pak choi is currently lacking in the existing literature. To address this knowledge gap, the current study was initiated to elucidate the genomic characteristics of bZIP genes, gain insight into their expression patterns during ER stress in pak choi, and investigate the protein-to-protein interaction of bZIP genes with the ER chaperone BiP. In total, 112 members of the BcbZIP genes were identified through a comprehensive genome-wide analysis. Based on an analysis of sequence similarity, gene structure, conserved domains, and responsive motifs, the identified BcbZIP genes were categorized into 10 distinct subfamilies through phylogenetic analysis. Chromosomal location and duplication events provided insight into their genomic context and evolutionary history. Divergence analysis estimated their evolutionary history with a predicted divergence time ranging from 0.73 to 80.71 million years ago (MYA). Promoter regions of the BcbZIP genes were discovered to exhibit a wide variety of cis-elements, including light, hormone, and stress-responsive elements. GO enrichment analysis further confirmed their roles in the ER unfolded protein response (UPR), while co-expression network analysis showed a strong relationship of BcbZIP genes with ER-stress-responsive genes. Moreover, gene expression profiles and protein–protein interaction with ER chaperone BiP further confirmed their roles and capacity to respond to ER stress in pak choi.

1. Introduction

Transcription factors (TFs) are the main players in regulating gene expression, serving essential functions in many biological processes within plants [1,2]. Until now, many TF families have been reported in plants [3]. One of the largest TFs family is the basic leucine zipper (bZIP) TF family [4,5]. Plant bZIP TFs family (bZIP genes) have diverse roles in developmental and physiological processes. These roles include ABA signaling for osmotic stress responses during vegetative growth [6], flowering time and seed germination [7], glucose-ABA signaling [8] lipid stress responses [9], response to zinc deficiency [10], sugar signaling during metabolism [11], activation of SA-dependent plant systemic defense responses, and JA- and ethylene-dependent defense mechanisms [12]. Furthermore, bZIP genes have been implicated in the modulation of signal transduction pathways and responses to a wide range of stresses. These stresses encompass drought, high salinity, cold stress, pathogen infection, osmotic stress, as well as ER stress [13,14,15]. Endoplasmic reticulum (ER) stress occurs when cells encounter an inequilibrium between the capacity to fold proteins and the demand for protein folding, resulting in the buildup of unfolded or misfolded proteins within the ER [16]. The bZIP genes play a vital role in regulating the UPR during ER stress [17]. The UPR is a cellular mechanism that is triggered when there is an accumulation of improperly folded or unfolded proteins within the ER [18].
In plants, bZIP genes have emerged as key regulators in response to ER stress, ensuring cellular homeostasis and survival under these challenging conditions [19]. The UPR in plants encompasses two functionally overlapping branches: IRE1-bZIP60 and bZIP17/bZIP28 [20], which are strongly associated with ER-responsive genes. The first branch of UPR involved IRE1, an ER receptor [21], acts as an endoribonuclease and a serine/threonine-protein kinase [22]. It mediates two distinct signaling pathways to regulate translation overload: the unconventional splicing of the bZIP60, and RNA cleavage through RIDD [23,24]. The N-terminal of IRE1 acts as a sensor for misfolded proteins, while the C-terminal serves as an RNA processing enzyme, specifically involved in unconventional bZIP60 splicing, a crucial regulator of the ER stress response [25]. While in the second branch, the bZIP17/bZIP28 proteins are characterized as type II transmembrane proteins, featuring a cytosolic N-terminal region containing the bZIP TF domain, while their C-terminus in the ER lumen ensures their retention within the ER. Under normal conditions, BiP interacts with bZIP17/28, retaining them in the ER [26]. However, during ER stress, BiP dissociates, facilitating the translocation of bZIP17/28 from ER to Golgi complex [27]. Subsequently, bZIP28 is cleaved by an unidentified protease, enabling the functioning of S2P. Conversely, S1P cleaves bZIP17. The cleaved forms of bZIP17/bZIP28 then translocated to the nucleus and form transcriptional complexes with nuclear TFs, leading to the activation of UPR genes [28]. Notably, both bZIP17/bZIP28 exhibit comparable characteristics and respond to various stimuli, including ER stress inducers, environmental cues, and developmental factors. These findings shed light on the intricate molecular mechanisms underlying the UPR in plants, emphasizing the interplay between bZIP genes and ER-stress-responsive genes.
BiP, on the other hand, is a binding protein abundant in the ER lumen, possesses an ATP-binding domain at its N-terminus, and a protein-binding domain at its C-terminus. This C-terminal domain enables BiP to bind to the hydrophobic surfaces of nascent proteins, thereby protecting them from aggregation through an ATP-dependent mechanism [29,30]. In response to ER stress induced by adverse environmental factors like heat and drought, or specific ER stressors such as TM and DTT, the expression of BiP genes is up-regulated through the UPR [22]. The overexpression of BiP genes has been demonstrated to enhance plant tolerance to environmental stresses. For instance, the overexpression of BiP genes is discovered along with the application of exogenous chemical chaperones such as sodium 4-phenylbutyrate (PBA), mitigated ER stress induced by DTT and high temperatures [31]. Moreover, the overexpression of soybean BiP in tobacco plants conferred tolerance to water deficit during plant growth by preventing endogenous oxidative stress [32]. The silencing of BiP genes in tomato compromised Ve1-mediated resistance to Verticillium dahlia [33], and the overexpression of BiP in soybean and tobacco plants resulted in hypersensitivity to Pseudomonas syringae pv tomato [34].
This study aimed to explore the genomic characteristics, expression patterns, and functional implications of BcbZIP genes in the context of ER stress response in pak choi (Brassica campestris ssp. chinensis), a leafy vegetable belonging to the Brassicaceae family. Pak choi is widely cultivated and consumed due to its nutritional value and culinary properties [35,36]. Understanding the molecular mechanisms underlying the ER stress response in pak choi can provide valuable insights into enhancing its stress tolerance and improving its overall quality. The objectives of this study are threefold. Firstly, we aimed to characterize the genomic organization and structural features of BcbZIP gene family in pak choi. This involved a genome-wide identification, physicochemical properties, phylogenetic analysis, gene structure organization, conserved domains and motif analysis, chromosomal arrangement and duplication events, divergence analysis, cis-element analysis, and GO enrichment analysis. Further protein–protein interaction network of BcbZIP genes with ER stress-responsive genes was also performed via string interaction network analysis. Secondly, we investigated the expression profiles of the BcbZIP genes in response to ER stress using RNA seq data (unpublished). Lastly, we experimentally investigated the role of BcbZIP genes in ER stress response. This involved subcellular localization and protein–protein interaction, both in vitro and in vivo, to explore the interaction and binding sites of BcbZIP60a and BcbZIP60b with ER chaperone BcBiP3, providing insights into the regulatory networks and signaling pathways involved in ER stress response in Pak choi.

2. Results

2.1. Total 112 BcbZIP Genes Were Identified and Their Physicochemical Properties Were Evaluated

In this study, 112 bZIP in pak choi termed as BcbZIP, after removing redundant sequences, were identified using HMM and BLASTp searches (see Materials and Methods). In order to comprehensively investigate the physicochemical characteristics of 112 identified BcbZIP genes, various parameters were evaluated in silico, and the results are presented in Supplementary File S1. The parameters analyzed included gene ID, location on chromosome, amino acids and CDS length, molecular weight (MW/kDa), isoelectric point (PI), GRAVY, formula, and predicted subcellular location. Analysis showed that BcbZIP genes were distributed within the genome from chromosome 1 to chromosome 10, and their start and end positions were specifically identified. However, the start and end position of the gene BraC06g046020.1 was not predicted. Among the BcbZIP genes, 57 genes were located on the reverse strand, 54 genes were located on the forward strand, while 1 gene did not have any available information in the NHCC database. Furthermore, the analysis revealed that amino acid (AA) length of BcbZIP genes varied from 120–780, while the CDS length ranged from 363–5728. The molecular weight (MW/kDa) of BcbZIP genes varied from 14,032.72–65,103.97, and the isoelectric point (PI) ranged from 4.98–10.11 PI. Additionally, the predicted subcellular localization analysis indicated that 63 BcbZIP genes were found in the nucleus, 33 in both the endoplasmic reticulum and nucleus, 9 in cytoplasm, 3 in the endoplasmic reticulum, and the remaining 3 genes were found in chloroplast, ER/cytoplasm, and ER/cytoplasm/nucleus, respectively. Overall, these results provide important understandings into the known basic parameters of the BcbZIP genes.

2.2. Phylogenetic Analysis Divided BcbZIP Genes into 10 Sub Families

In order to conduct a more comprehensive analysis of the evolutionary relationship among BcbZIP genes, an un-rooted phylogenetic tree was constructed using the 70 protein sequences of AtbZIP and 112 identified BcbZIP genes with 1000 bootstrap values using the neighbor joining method. The phylogenetic tree divided the bZIP genes into 10 sub families. i.e., A, B, C, D, E, I, S (S1 and S2), G, F, and H based on Arabidopsis sub groups. Within subfamily A, the 13 AtbZIP genes were clustered with the 21 BcbZIP genes. In subfamily B, four AtbZIP genes were grouped with the five BcbZIP genes. In subfamily C, four AtbZIP genes were grouped with the seven BcbZIP genes. In subfamily D, 9 AtbZIP genes were grouped with the 20 BcbZIP genes. In subfamilies E and I, 13 AtbZIP genes were grouped with the 19 BcbZIP genes. In subfamily S, 18 AtbZIP genes were grouped with the 32 BcbZIP genes. In subfamily G, six AtbZIP were grouped with the three BcbZIP genes, and in subfamilies F and H, four AtbZIP genes were grouped with the five BcbZIP genes. Overall, these findings offer valuable insights into the evolutionary connections between AtbZIP and BcbZIP genes (Figure 1).

2.3. The Chromosomal Location and Duplication Events of BcbZIP Genes

Chromosomal distribution and duplication of BcbZIP genes were investigated and visualized on a circos plot (Figure 2). Results revealed that out of 112 BcbZIP genes, there was uneven distribution across the 10 chromosomes: with chromosome 1 containing 7 BcbZIP genes, each chromosome 2, 3, and 6 containing 14 BcbZIP genes, each chromosome 4, 7, and 10 containing 9 BcbZIP genes, chromosome 5 containing 8 BcbZIP genes, chromosome 8 containing 6 BcbZIP genes, and chromosome 9 containing 20 BcbZIP genes. The observed multigene families could have arisen from region-specific duplication or genome-wide polyploidization. This evolutionary mechanism has been demonstrated as a significant aspect of plant genome evolution. Additionally, 38 pairs of similar paralogues were identified and grouped in the same sub clade, implying that these gene duplicates originated from duplication events. This approach provides a reliable and standardized approach for assessing gene duplication events and their chromosomal distribution.

2.4. Divergence Analysis Investigated How BcbZIP Genes Have Evolved and Diversified over Time

In order to gain a better understanding of the evolutionary characteristics of BcbZIP genes, a divergence analysis was conducted. This involved calculating the ratio of Ka/Ks for each pair of paralogous BcbZIP genes. Total 38 BcbZIP paralogous genes were identified with a Ka/Ks calculator (Supplementary File S2, Figure S6). The results indicated that Ka divergence values for different paralogous pairs ranges from 0.001699–0.308732, Ks divergence values ranges from 0.017292–1.058908, while Ka/Ks divergence value ranges from 0.06311–1.004532. Notably, the Ka/Ks ratio can be utilized for assessing selective pressure on genes in molecular biology. Overall, most of the gene pairs (99.2%) had a Ka/Ks ratio of less than 1, showing purifying selection during the evolution of most bZIP genes in this family. For each paralogous pair of BcbZIP genes, the divergence time was found to be between 0.73–80.71 MYA (Table 1). This approach provides a valuable and standardized methodology for exploring the evolutionary dynamics of gene families and their diversification through time.

2.5. Gene Structure, Domains, and Motifs Analysis Provide a Genetic Basis of Biological Processes to Infer the Potential Functions of BcbZIP Genes

To better understand the basic functions of identified BcbZIP genes, the protein and nucleotide sequences were analyzed for conserved domains, gene structure organization, and motifs using TBtools. Pfam protein analysis and sequence analysis showed that all genes contained a bZIP domain. The specific bZIP domains found in all BcbZIP genes included bZIP_plant_BZIP46, bZIP superfamily, bZIP_HBP1b-like, bZIP_HY5-like, bZIP_plant_RF2, bZIP_plant_GBF1, bZIP_C superfamily, and bZIP_C. Additionally, ten different motifs were identified by using MEME suite software 5.4.1 corresponding to bZIP domains to explore their structural and functional diversity (Supplementary File S2, Figure S1). Moreover, the subfamily S (S1 and S21) contain motif 1 and 6 following three domains (bZIP plant GBF1, PRK 13,875 super family, and bZIP super family) (Supplementary File S2, Figure S2). The subfamily C, G, and A contain motif 1, 6, 7, 9, and 10 following 12 domains (bZIP C, bZiP superfamily, bZiP plant GBF1, bZIP C superfamily, AMN1 superfamily, F-box SF superfamily, MFMR, bZIP1, DUF6515 superfamily, MFMR assoc superfamily, BRLZ, and bZIP plant BZIP46) (Supplementary File S2, Figure S3). The subfamily I, E, F, H, D, and B contain motif 1, 2, 3, 4, 5, 6, 8, and 10 following 12 domains (bZiP plant RF2, COG1579 superfamily, ZapB superfamily, SMC prok B superfamily, ATG16 superfamily, HAP1 N superfamily, Smc superfamily, ZapB, bZIP HY5 like, DOG1, bziP superfamily, bZIP HBP1b like, PHA03247 superfamily) (Supplementary File S2, Figure S4).
The structural organization of genes further revealed the arrangement of untranslated regions (UTR) and coding regions (CDS) in 112 BcbZIP genes. The gene structure organization showed uneven distribution of UTR and CDS regions, suggesting that the introns and exons were highly variable in BcbZIP genes. Subfamily S had 3 genes having both UTR and CDS, while 29 genes had only CDS regions. Subfamily C, G, and A had 14 genes having both UTR and CDS, while 16 genes had only CDS regions. Subfamily I, E, F, H, D, and B had 22 genes having both UTR and CDS, while 27 genes had only CDS regions (Supplementary File S2, Figure S5).

2.6. Cis Elements Analysis Indicate the Potential of BcbZIP Genes to Mediate Responses to a Diverse Range of Environmental Stimuli

BcbZIP genes revealed the presence of numerous cis-elements in their 1500 bp upstream promotor sequences, including light, hormone, stress, and plant growth and development related cis-elements. Analysis identified a total of 40 photo-responsive cis-elements, including 3-AF1 binding site, ACE, GT1 motif. Box-4, I-box, G-box, TCT motif, Sp1, TCCC motif, A-box, AAAC-motif, ACA-motif, AE-box, AT1-motif, ATC-motif, Box II, CAG-motif, CCAAT-box, chs-CMA1a, chs-CMA2a, chs-CMA2b, chs-Unit 1 m1, GA-motif, Gap-box, GATA-motif, GATT-motif, GGA-motif, GTGGC-motif, LAMP-element, L-box, LS7, MBS, MBSI, MRE, P-box, RY-element, TC-rich repeats, 4cl-CMA1c, and 4cl-CMA2b. Additionally, the promoter region contains cis-elements that are involved in regulating plant responses to different stresses, including LTR, MBS, TCA-element, and TC-rich repeats. Moreover, 13 hormone-responsive elements like TGA elements. TGA box, ABRE, TATC-box, GARE-motif, ERE, TCA-element, CGTCA-motif, AuxRE, AuxRR-core, ARE, and TGACG-motif, which can bind to regulators in response to hormone signals. Furthermore, 17 cis-elements, Circadian, CAT-box, O2-site, MSA-like, AACA motif, ARE, AT-rich element, CAAT-box, GCN4_motif, HD-Zip 1, HD-Zip 3, motif I, WUN-motif, RY-element, CCAAT-box, and MBSI were also identified in the promoter region, which play a crucial role in the binding with regulators that control plant growth and development. The results indicate that BcbZIP genes possess the capability to regulate responses to different environmental stimuli. This is attributed to the presence of a wide range of cis-elements in their promoter region that are responsive to light, hormones, stress, as well as plant growth and development. (Figure 3).

2.7. GO Enrichment Analysis Suggest the Crucial Roles of BcbZIP Genes in Regulating Multiple Cellular Processes

To further discover the essential role of BcbZIP genes in regulating multiple cellular responses, we analyzed the 112 BcbZIP genes for GO enrichment. The results of GO enrichment analysis demonstrated that the BcbZIP genes share a common set of biological functions. Specifically, a majority of BcbZIP genes were identified as being involved in diverse molecular functions and biological processes including, but not limited to, response to xenobiotic stimulus, endoplasmic reticulum-unfolded protein response, protein dimerization, protein heterodimerization, abscisic acid-activated signaling pathway, calcium-mediated signaling, response to mechanical stimulus, and protein homodimerization, as illustrated in (Figure 4A). These findings suggest that the BcbZIP genes serve as crucial regulatory factors in a multitude plants cellular processes.

2.8. Co-Expression Network Conveyed a Strong Association between BcbZIP Genes with ER Stress Responsive Genes

To further elucidate the contribution of BcbZIP genes in ER stress, another BLASTp search was conducted using Arabidopsis protein sequences of ER stress responsive genes (AT2G17520, AT5G24360, AT5G28540, AT1G09080, AT5G61790, AT1G72280, AT1G65040, AT1G18260, AT4G29330, and AT3G17000 annotated as ATIRE1A, AtIRE1B, AtBiP1, AtBiP3, AtCNX, AtERO1 HRD1, SEL1, DER1, and UBC32, respectively) to identify its homologues in pak choi. Insight into the potential association between BcbZIP genes and ER stress responsive genes was obtained through the analysis of AtbZIP genes using STRING software v12.0, resulting in a visual map (Figure 4B). The homologues of BcbZIP genes based on potential co-expressions of AtbZIP genes in the string network confirmed a significant connection between 5 BcbZIP genes and 10 ER stress responsive genes, with a p-value of <1.0 × 10−16. Interaction networks were further analyzed for protein–protein interactions that shared biological processes, molecular function, and cellular components. Edges/lines of varying colors were used to represent strong versus weak interactions among proteins. The colored lines linking the nodes depict the interactions between proteins of the genes, highlighting the protein–protein interactions within the network. These findings revealed a strong association between 5 BcbZIP genes and 10 ER-stress-responsive genes.

2.9. Expression Profiles of BcbZIP Genes during ER Stress in Pak Choi

To explore the expression patterns of the bZIP gene family in pak choi under ER stress conditions, we utilized transcriptome profiling data obtained through RNA-Seq analysis. Through this analysis, we observed distinct expression patterns within the bZIP genes, which allowed us to classify them into four distinct groups. Notably, genes in groups 1, 2, and 4 exhibited elevated expression levels under ER stress conditions. On the other hand, genes in groups 2 and 3 showed increased expression in the ER stress suppression group, when treated with the ER stress inhibitor, tauroursodeoxycholic acid (TT). These findings provide valuable insights into the dynamic regulation of the bZIP gene family in response to ER stress in pak choi (Figure 5 and Supplementary File S3).

2.10. Subcellular Localization Revealed the Presence of BcbZIP60a and BcbZIP60b in Nucleus

The subcellular localization of BcbZIP60a and BcbZIP60b was investigated to gain a better understanding of their functions. In the present study, the leaf cells of N. benthamiana were transformed with BcbZIP60a: GFP and BcbZIP60b: GFP constructs. Confocal laser imaging revealed that both BcbZIP60a and BcbZIP60b, fused with GFP, emitted green fluorescence in the nucleus of tobacco cells, indicating their localization in the nucleus, suggesting their potential roles in nuclear processes (Figure 6). Understanding the subcellular localization of proteins is crucial for unraveling their functional significance and can contribute to our knowledge of cellular processes and molecular interaction.

2.11. Y2H Displayed a Strong Protein–Protein Interaction of BcbZIP60a and BcbZIP60b with BcBiP3

In this study, the transcription activation of BcbZIP60a and BcbZIP60b was observed. Recombinant plasmids containing full-length CDS BcbZIP60a and BcbZIP60b fused with the GAL4 DNA-binding domain (BD-BcbZIP60a and BD-BcbZIP60b) were constructed and introduced into yeast strains. The results demonstrated that BD-BcbZIP60a and BD-BcbZIP60b exhibited strong transcription activation activity and activated the expression of reporter genes. This was evident from the growth of yeast colonies on specific medium, while the negative control (BD-PGBKT7 empty vector) showed no growth. Additionally, to investigate the transcriptional mechanism of BcbZIP60a and BcbZIP60b in response to ER stress, the full-length CDS BcBiP3 was introduced into the Gal4 activation domain of prey vector (AD-BcBiP3). Co-transformation of yeast strains with BD-BcbZIP60a, BD-BcbZIP60b, and AD-BcBiP3 revealed that only the yeast co-transformed with BcbZIP60a and/or BcbZIP60b along with BcBiP3 could survive under specific conditions. This indicates a strong protein–protein interaction between BcbZIP60a, BcbZIP60b, and BcBiP3. These results highlights valuable insights into the role of BcbZIP60a and BcbZIP60b as TFs and their involvement in response to ER stress (Figure 7). The study underscores the significance of bZIP genes in regulating gene expression and their potential as targets for enhancing plant stress tolerance.

2.12. BiFC Assays Indicate the Interaction of BcbZIP60a and BcbZIP60b with BcBiP3 at Multiple Points

To investigate the interaction between BcbZIP60a and BcBiP3, as well as between BcbZIP60b and BcBiP3 in living cells, we employed BiFC assays. The full-length CDS of BcbZIP60a, BcbZIP60b, and BcBiP3 were cloned into both YNE and YCE vectors, respectively, to facilitate the BiFC assays. The constructed vectors were then transformed into A. tumefaciens. Subsequently, different combinations of these constructs were mixed at 1:1 ratio and infiltrated into one-month-old tobacco epidermal cells. Confocal fluorescence microscopy was used to visualize the results. Positive BiFC interaction signals were observed between BcbZIP60a-YNE + BcBiP-YCE and BcbZIP60a-YCE + BcBiP-YNE, indicating an interaction between BcbZIP60a and BcBiP3. Similarly, GFP signals were detected between BcbZIP60b-YNE + BcBiP-YCE and BcbZIP60b-YCE + BcBiP-YNE, suggesting an interaction between BcbZIP60b and BcBiP3. These findings indicate that both BcbZIP60a and BcbZIP60b can interact with BcBiP3 at multiple points, as evidenced by the positive BiFC signals. To serve as negative controls for the BiFC assay, combinations such as YCE + YNE, BcbZIP60a-YNE + YCE, BcBiP-YCE + YNE, BcbZIP60b-YNE + YCE, and BcBiP-YCE + YNE were used. None of these combinations exhibited green fluorescence signals in tobacco epidermal cells, further confirming the specificity of the observed interactions (Figure 8).

3. Discussion

bZIP genes are unique in its structure containing a conserved bZIP domain [37]. To date, genome-wide investigations in numerous plants have been used to predict or identify the bZIP genes. A total of 75 bZIP genes have been identified in A. thaliana ([38]. A number of grass family (Gramineae) species have also had their genes characterized, including 187 genes in Triticum aestivum [39], 92 in Sorghum bicolor [40], 89 in Oryza sativa [41], 125 in Zea mays [42], and 96 in Brachypodium distachyon [43]. Extensive research has led to the discovery and comprehensive examination of numerous bZIP genes within brassica species including B.napus [44], Chinese cabbage [45], B. oleraceae [46], and B. rapa [47]. However, despite the extensive research on genomic characterization of bZIP genes in multiple plants, our understanding of these genes in pak choi is limited. To address this knowledge gap, we utilized the NHCC database of brassica species to conduct a comprehensive investigation into the genomic characterization of bZIP genes in pak choi.
In order to gain a more comprehensive understanding of the evolutionary history of the BcbZIP genes in pak choi, the phylogenetic analysis resulted in the clustering of these genes into 10 distinct subfamilies (Figure 2). This classification scheme is consistent with previous findings from similar studies on bZIP gene families in numerous other plant species, including Arabidopsis [38], Sorghum [40], Cassava [13], and Grapevine [48]. The most BcbZIP genes were found in subgroup S, followed by subgroups A and D, while the least BcbZIP genes were found in subgroup H. These findings exhibit similarities to the observations made in G. biloba [49], A. thaliana [50], Populus [51], R. sativu [52], B. napus, and O. europaea [53], which contains the most bZIP members in S, A, I, and D subclasses. This suggests that organization of bZIP genes into subfamilies is evolutionarily conserved across different plant species. The classification of bZIP genes into subfamilies provides a framework for understanding their functional diversity and potential roles in different biological processes. Moreover, BcbZIP genes belonging to the same subgroup exhibit a notable degree of similarity in gene structure, including the number of introns and exons, as well as the distribution of motifs [49].
The organization of exons and introns in a gene indicates the evolutionary path of gene families [54,55]. In this study, an analysis was conducted on the gene structures of 112 BcbZIP genes, which revealed a consistent pattern within each group while exhibiting significant variation between different groups (Figure S5). Apart from the bZIP domain, several additional domains were also found in bZIP genes (Figures S2–S4). These results suggest that various conserved motifs outside the bZIP domain could have different roles in determining the functions of bZIP proteins [56,57]. Similarly, BcbZIP genes were distributed across all 10 chromosome in pak choi (Figure 3). This distribution is previously been confirmed in B. rapa [46] and B. napus [44]. Furthermore, tandem/segmental duplications are vital mechanisms that contribute to expansion and diversification of gene families by replicating genes with in the same genomic region or across different chromosomal segments, increasing gene copy numbers. Duplication events are known to play significant roles in gene families expansion [58]. In the current investigation, 38 segmental duplication pairs were recognized in pak choi, as depicted in (Figure 3 and Table 1). These findings suggest that the expansion of the BcbZIP gene family primarily originated from segmental duplications. Additionally, it is noteworthy that the Ka/Ks ratios were found to be lower than 1, indicating that these duplicated BcbZIP genes likely underwent purifying selection and have been conserved in their functions throughout evolution [59,60].
Functional enrichment analysis is a powerful computational method used to interpret gene expression data and identify pathways and processes associated with specific gene sets or biological entities [61]. According to the results of enrichment analyses of BcbZIP genes (Figure 5A). These pathways include hormone responses to xenobiotic stimulus, ER UPR, protein dimerization activity, protein heterodimerization activity ABA-activated signaling pathway, calcium-mediated signaling, mechanical stimulus, and protein homodimerization activity [62,63]. The BcbZIP genes have been identified as key regulators in diverse biological processes, including their involvement in the response to ER stress. To gain a deeper understanding of the molecular mechanisms underlying the ER stress response, a protein–protein interaction network analysis was conducted using STRING [59,60,64]. This analysis allowed for the visualization and exploration of protein networks based on functional enrichment analysis (Figure 5B). The ER stress response is primarily intermediated through the UPR pathway, which activates specific genes and signaling pathways.
The bZIP genes are primarily associated with TFs and play roles in regulating gene expression and important biological processes. These genes are involved in the pathways through which bZIP genes control and modulate gene expression [62]. The UPR pathway can be initiated by the accumulation of misfolded proteins within the ER. This pathway involves the participation of bZIP genes as well as other genes that are responsive to ER stress (Figure 5B). In the present study, the expression profiles of BcbZIP genes were elucidated in response to TM induced ER stress (TM) as well as with the application of TUDCA prior to TM treatment (TT) in pak choi (Figure 6). The expression profiles of most of BcbZIP genes were increased in TM. The significant upregulation of these genes in response to TM indicated their involvement in UPR. The protein–protein interaction network of BcbZIP genes with ER stress-responsive genes is instrumental in unraveling the physical contacts and interactions among BcbZIP and other proteins implicated in ER stress response in the UPR pathway. During ER stress in plant cells, there is an interplay between bZIP60 and BiP. BiP proteins, recognized for their pivotal involvement in protein translocation and folding processes, are prominently induced by the UPR, and serve as a distinctive indicator of ER stress in both animal and plant systems [65,66]. Disruption of protein folding in the ER leads to induction of genes for ER-resident chaperones, including BiP, as part of the ER stress response. However, upon detection of unfolded proteins, BiP is released and binds to unfolded proteins, leaving IRE1 free to oligomerize and splice bZIP60 mRNA. This results in the activation of bZIP60 as a TF [67]. By elucidating these molecular interactions, we further comprehend the intricate regulatory mechanisms at play during ER stress. Correspondingly, to gain a comprehensive understanding of the role of bZIP genes in the ER pathway, our study focused on examining the interaction between BcbZIP60a and BcbZIP60b genes (representatives of BcbZIP genes) and the prominent ER chaperone, BiP3, which shed light on the molecular mechanisms involved in this pathway. To investigate this interaction, we employed the Y2H assay, which demonstrated a robust association between both BcbZIP60a and BcbZIP60b with BcBiP3 (Figure 8). This suggests that bZIP genes play an essential role in the regulation of ER function, potentially influencing protein folding, quality control, and ER stress response. To further validate these findings, we conducted a BiFC assay, which provided additional insights into the interaction of both BcbZIP60a and BcbZIP60b with BcBiP3, specifically on both YNE and YCE terminals. This indicates that the interaction between these bZIP genes and BcBiP3 occurs at multiple sites within the ER, further emphasizing their importance in ER homeostasis (Figure 9). BcbZIP60a and BcbZIP60b are involved in the UPR, which is a signaling pathway that up-regulates the expression of ER chaperones like BcBiP3 during ER stress. This suggest that under normal conditions, bZIP proteins are bound to the ER membrane and maintained in an inactive state by the chaperone protein BiP. However, during ER stress, BiP is sequestered by the accumulation of misfolded proteins, leading to the activation of bZIP genes [67]. Once activated, bZIP proteins translocate to the nucleus and bind to specific DNA sequences known as ER stress response elements (ERSEs) present in the promoters of target genes [28]. This binding triggers the up-regulation of genes involved in various aspects of the UPR, including ER-associated degradation (ERAD), which helps in clearing misfolded proteins, and the synthesis of ER chaperones, which assist in protein folding [68]. Our results also confirmed the nuclear localization of BcbZIP60a and BcbZIP60b, as shown in (Figure 7). Moreover, bZIP genes also regulate the expression of genes involved in lipid metabolism, redox homeostasis, and apoptosis [69].
The comprehensive results presented in this research offer compelling evidence of the participation of BcbZIP genes in pathways related to ER stress tolerance. Moreover, the functional characterization of these genes highlights their indispensable roles in the UPR. These observations form a crucial foundation for the genetic screening and engineering of novel bZIP genes with enhanced ER stress tolerance in pak choi.

4. Materials and Methods

4.1. Study Layout and Plant Growth Conditions

The Arabidopsis Information Resource (TAIR) database ftp://ftp.arabidopsis.org) (accessed on 12 March 2023), and the newly developed NHCC database http://tbir.njau.edu.cn/NhCCDbHubs/ (accessed on 15 March 2023), were used to retrieve bZIP genes from the genomes of Arabidopsis thaliana (V.10) and pak choi (V 1.0), respectively. The data obtained were then implemented to undergo in silico characterization of bZIP genes using advanced bioinformatics analysis. To further perform wet lab experiments for the differential expression levels of bZIP genes during ER stress, seeds of pak choi (variety Ziguan) were germinated on pre-soaked filter paper in Petri dishes and subsequently transplanted into vermiculite-containing planting trays in controlled conditions (16 h light and 8 h dark, relative humidity 60%, Av. Temp. 18–24 °C). The plants at 4 to 5 leaf stage were then stratified into three individual groups: those left untreated, served as controls (CK); those induced with ER stress using 5 μg/mL tunicamycin treatment, marked as TM; and plants treated with 25 μg/mL tauroursodeoxycholic acid (TUDCA), as an ER stress suppressor, for 5 days prior to TM treatment, marked as TM + TUDCA [70]. Leaf samples were collected after 72 h of treatment, frozen in liquid nitrogen immediately, and sent to company for RNA sequencing. To conduct a more in-depth analysis of bZIP genes role in the ER stress pathway, the chosen bZIP genes, along with the highly abundant ER chaperone BiP3, were cloned into specific vectors. This was done in order to carry out experiments that investigate protein–protein interactions and determine the subcellular localization of these genes (Figure 9).
Plants 13 01160 g009
Figure 9. Graphical illustration presenting a comprehensive analysis of molecular characterization of bZIP genes, including expression patterns and functional implications during ER stress.
Figure 9. Graphical illustration presenting a comprehensive analysis of molecular characterization of bZIP genes, including expression patterns and functional implications during ER stress.
Plants 13 01160 g009

4.2. Identification and Physicochemical Analysis of bZIP Genes

Two methods were initiated to find the candidate orthologous of bZIP genes in pak choi. Firstly, BLASTp (E-value 1 × 10−5) search was conducted using the protein sequences of AtbZIP genes as queries keeping the pak choi genome as database to get the candidate orthologous of bZIP genes. To further reassure the members of bZIP genes in pak choi, a reciprocal BLASTp was conducted using the candidate orthologous of pak choi as queries while keeping the AtbZIP genes as candidates. The resulting members were then considered as the homologues of AtbZIP genes in pak choi [71]. Secondly, the identified candidate homologues of AtbZIP genes in pak choi were further confirmed via HMMER 3.0 http://hmmer.janelia.org/ (accessed on 16 April 2023), using the bZIP domain file PF00170.22 against the pak choi genome [64]. To remove redundancy, the candidate homologues were further confirmed by performing bZIP domains annotation via MOTIF search https://www.genome.jp/tools/motif/ (accessed on 16 April 2023), NCBI conserved domain database http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi (accessed on 16 April 2023), SMART database http://smart.embl-heidelberg.de/ (accessed on 16 April 2023), and Pfam database http://pfam.janelia.org/ (accessed on 16 April 2023). The final candidate homologues of bZIP genes in pak choi were then annotated as BcbZIP genes. Furthermore, the physicochemical properties including amino acids, molecular weight, PI, GRAVY, and formula were determined using the ExPASy-ProtParam tool http://web.expasy.org/protparam/ (accessed on 16 April 2023) [72]. The in silico subcellular localization was determined through the use of a predictive tool available at https://predictprotein.org (accessed on 16 April 2023).

4.3. Multiple Sequence Alignment and Phylogenetic Analysis of BcbZIP Genes

To further get insights into phylogeny of BcbZIP genes, 70 protein sequences of AtbZIP genes, except three sequences, i.e., At3g17610 (HYH), AT2G12980 (AtbZIP32), and AT2G13130 (AtbZIP73), which were drawn out because of non-availability, and the 112 of BcbZIP protein sequences, except the redundant sequences (BraC08g022000.1, BraC05g001930.1, BraC09g063720.1, BraC05g009850.1, BraC01g002060.1, BraC06g034200.1, BraC03g018730.1, and BraCxxg010020.1), satisfying all the requirements, were aligned using multiple sequence alignment tool MUSCLE https://www.ebi.ac.uk/Tools/msa/muscle/ (accessed on 2 May 2023) with default settings to get most accurate alignment. The tree was then generated by MEGA 11 software using the neighbor joining model, with 1000 bootstrap values [73].

4.4. Chromosomal Location and Duplication of BcbZIP Genes

The chromosomal distribution of 112 BcbZIP genes were identified based on the chromosomal information provided in the NHCC database http://tbir.njau.edu.cn/NhCCDbHubs/ (accessed on 17 May 2023). The synteny analysis between 112 BcbZIP genes were done using the BLASTp algorithm, and gene duplication or synteny events were evaluated with the Multiple Collinearity Scan toolkit (MCScanX) using a default parameter, and the visualization was created by the circos. The circos plot was then generated via circos visualizing tool in TBtools software v2.056 [74] from the available chromosome length, location of bZIP genes on chromosome, and linked genes regions showing the chromosomal location and duplication in pak choi [75].

4.5. Gene Structure, Domains, and Motifs

To perform a thorough analysis of the domains present in BcbZIP proteins, the corresponding protein sequences were exposed to domain analysis using the NCBI CDD online software (accessed on 20 May 2023). The resulting predicted domain information was then used for the visualization of domain information using the TBtools software. Additionally, conserved motif analyses of the BcbZIP proteins were carried out using MEME suite software v5.4.1 https://meme-suite.org/meme/tools/meme (accessed on 2 June 2023) [76], identifying 10 conserved motifs, and further visualized via TBtools software. Consequently, to visualize the gene structure organization, TBtools software was used. This involved submitting the gff3 files of the pak choi genome, along with a list of identified gene IDs. This approach provide a comprehensive analysis for the domains, motifs, and gene structure organization of BcbZIP proteins.

4.6. Divergence, Cis Elements, and GO Enrichment Analysis

To further check the BcbZIP genes for synonymous and non-synonymous changes and their divergence through time, the Ka/Ks calculator http://services.cbu.uib.no/tools/kaks (accessed on 8 June 2023) [77] was utilized to compute Ka/Ks values in DNA of BcbZIP genes. The divergence time was then calculated in TMY (time in million years) using the following formula;
T i m e   o f   d i v e r g e n c e   T = S y n o n y m o u s   s u b s t i t u t i o n   r a t e   d S   or   K s 2 × D i v e r g e n c e   r a t e   ( 6.56 × 10 − 9 ) × T M Y   ( 10 − 6 )
For specific genes, cis-acting regulatory elements were identified by retrieving the promoter sequences of BcbZIP, which were 1500 bp upstream, from the pak choi genome based on generic file format (GFF). PlantCARE tool https://bioinformatics.psb.ugent.be/webtools/plantcare/html/ (accessed on 20 June 2023) was used to identify these regulatory elements [78]. The GO enrichment Analysis was done by submitting the gene IDs of BcbZIP in NHCC online database http://tbir.njau.edu.cn/NhCCDbHubs/ (accessed on 20 June 2023), using the GO enrichment Analysis tool.

4.7. Co-Expression Network Analysis of BcbZIP Genes with ER Stress Responsive Genes

To generate a co-interaction network of bZIP genes along with ER stress pathway genes, the protein sequences of the bZIP genes and ER stress pathway genes were utilized. This analysis was conducted using String https://cn.string-db.org/ (accessed on 25 June 2023). Furthermore, in order to detect homologous sequences within the pak choi genome, a BLAST search was performed using the protein sequences of key genes implicated in the ER stress pathway in Arabidopsis as queries. Homologous sequences were determined based on their substantial e-value of 1 × 10−10, and these sequences were subsequently regarded as the most promising hits and selected as homologs. BcbZIP genes along with homologues sequences of Arabidopsis, were further subjected to co-interaction analysis and functional annotation in String database. This analysis involved leveraging the available transcriptomic data of Arabidopsis to gain insights into the co-expression patterns and potential functional associations of identified genes. The methods employed in this study were based on previously established approaches described by [79].

4.8. Expression Analysis of BcbZIP in Response to ER Stress

An experiment was conducted to analyze the expression of BcbZIP genes in pak choi under ER stress. The experiment involved three treatment groups: a control group (CK) with no chemical treatment, a group exposed solely to TM to induce ER stress (TM group), and a group that received a TUDCA pretreatment for five days followed by TM application to alleviate ER stress (TM + TUDCA group) [70]. Leaf specimens were collected 72 h after exposure to ER stress, with three independent biological replicates to ensure result reliability and accuracy. The RNA extraction, library construction, and RNA sequencing were outsourced to a service company (Sangon biotech, Shanghai, China). Total RNA was extracted using TRNzol Reagent following the manufacturer’s instructions. The integrity of the extracted RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). The nine libraries were sequenced on an Illumina Hiseq platform using 150 bp paired-end sequencing.

4.9. Yeast Two Hybrid (Y2H) Assay of BcbZIP60 with ER Chaperone BcBiP3

The Yeast two hybrid (Y2H) assay was performed following the guidelines provided by the Matchmaker Gold. To create prey construct, the CDS of BcBiP3 was fused with the pGADT7 (AD) vector using the EcoRI and BamHI cleavage sites, resulting in the generation of pGADT7: BcBiP3. Similarly, the CDS of BcbZIP60a and BcbZIP60b were fused with the pGBKT7 (BD) vector to create pGBDT7: BcbZIP60a and pGBDT7: BcbZIP60b as bait constructs. Following that, the bait and prey plasmids were co-introduced into the Y2H Gold yeast strain and cultured on SD/-Trp Leu medium for 80 h. Subsequently, the cells were transferred to a selective medium, specifically SD/-Trp-His-Leu-Ade, which was supplemented with AbA (400 ng/mL) from Takara (Shiga, Japan). The cells were incubated in this medium for a duration of 80 to 90 h [80]. The primers used for the Y2H assay of BcbZIP60a, BcbZIP60b, and BcBiP3 are given in Supplementary File S4.

4.10. BiFC Assay of BcbZIP60 with ER Chaperone BcBiP3

The BiFC assay was performed based on a previous study [81]. The coding sequence of BcbZIP60a, BcbZIP60b, and BcBiP3 were merged to both the N-terminus of GFP (SPYNE) and the C-terminus of GFP (SPYCE). Subsequently, combinations BcbZIP60a-YNE/BcBiP3-YCE, BcbZIP60a-YCE/BcBiP3-YNE, BcbZIP60b-YNE/BcBiP3-YCE, and BcbZIP60b-YCE/BcBiP3-YNE were co-injected into tobacco leaves. SPYNE and SPYCE empty vectors were used as negative controls. The emitted green fluorescent protein (GFP) signal was detected using a Confocal Laser Scanning Microscope. The fluorescence was observed at a wavelength of 488 nm. The primers used for the BiFC of BcbZIP60a, BcbZIP60b, and BcBiP are given in Supplementary File S4.

4.11. Subcellular Localization of BcbZIP60

To conduct subcellular localization assays, the coding regions of BcbZIP60a and BcbZIP60b were inserted into pCAMBIA 1300 vector containing the GFP reporter, resulting in the generation of BcbZIP60a-GFP and BcbZIP60b-GFP constructs. Additionally, the pCAMBIA 1300 vector was transformed as a control. The recombinant vectors, along with the control vector, were introduced into A. tumefaciens strain GV3101 and infiltrated into tobacco leaves. Subsequently, fluorescence signals were observed using a confocal microscope (LSM800, Zeiss, Germany) to determine the subcellular location of the proteins. [80,82]. The primers used for the subcellular localization of BcbZIP60a and BcbZIP60b are given in Supplementary File S4.

5. Conclusions

In conclusion, the phylogenetic analysis discovered that the 112 BcbZIP genes were significantly expanded and classified into 10 subfamilies based on sequence similarities. These genes were unevenly distributed across 10 chromosomes and duplicated during evolution, with a divergence analysis confirming their time of divergence ranging from 0.73 to 80.71 MYA. Domain and motif analyses confirmed the presence of bZIP domains in BcbZIP genes, with gene structural organization revealing highly diverse exon and intron arrangements. Additionally, a wide range of cis-elements were detected in the promoter region of BcbZIP genes comprising light, hormone, stress, and plant growth and development responsive elements. GO enrichment analysis confirmed their roles in ER UPR. The co-expression network analysis demonstrated a strong association of BcbZIP genes with ER-stress-responsive genes. Expression profiles of BcbZIP genes and functional identification via protein–protein interaction further supported their involvement in ER stress response in pak choi. Future directions for this study could involve investigating the functional significance of expanded bZIP gene families in other plant species and exploring their roles in response to different environmental stimuli. Additionally, studying regulatory mechanisms governing the expression of bZIP genes and their interaction networks in greater detail could provide further insights into ER stress and its implications for plant growth and development.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/plants13081160/s1, The physicochemical properties of 112 identified BcbZIP genes (File S1); Domains, motifs, Sequence logos of motifs, and Gene structure Organization of BcbZIP genes (File S2); TPM values of expression of BcbZIP genes (File S3); Primers used in this study (File S4).

Author Contributions

Conceptualization, Methodology, Formal Analysis (A.A. and A.J.); Data validation and curation (X.Z., X.H. and K.A.K.); Writing- Original draft of the manuscript (A.A.); Writing—Review and Editing (A.J.), Resources and supervision (C.H. and Y.L.). All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by China’s national science and technology basic resources survey project (2023FY101202), and China’s national vegetable industry technology system (CARS-23-A-16).

Data Availability Statement

The data supporting the results are already given in the main text and Supplementary Files.

Acknowledgments

The first author of the paper is very grateful to China Scholarship Council (CSC) for providing funds for perusing her PhD studies from the College of Horticulture, Nanjing Agricultural University Nanjing 210095, Jiangsu, China. The authors extend their appreciation to the Deanship of Scientific Research at King Khalid University Saudi Arabia for funding this work through Large Groups Project under grant number RGP2/132/45.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. Phylogenetic analysis of bZIP genes in pak choi and Arabidopsis. (A) The phylogenetic tree divided into 10 sub families based on Arabidopsis sequences. (B) The heatmap of number of bZIP genes in each subfamily of pak choi and Arabidopsis.
Figure 1. Phylogenetic analysis of bZIP genes in pak choi and Arabidopsis. (A) The phylogenetic tree divided into 10 sub families based on Arabidopsis sequences. (B) The heatmap of number of bZIP genes in each subfamily of pak choi and Arabidopsis.
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Plants 13 01160 g002
Figure 2. The collinearity and distribution of 112 BcbZIP genes. The chromosomal distribution of 112 BcbZIP genes are illustrated on 10 chromosomes along the circumference of the circle. The different colored lines within the circle represent collinearity relationships among BcbZIP genes.
Figure 2. The collinearity and distribution of 112 BcbZIP genes. The chromosomal distribution of 112 BcbZIP genes are illustrated on 10 chromosomes along the circumference of the circle. The different colored lines within the circle represent collinearity relationships among BcbZIP genes.
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Plants 13 01160 g003
Figure 3. Cis-regulatory elements of BcbZIP genes. (A) Total number of cis-elements found in 112 BcbZIP genes. (B) Stress-responsive elements found in 112 BcbZIP genes. (C) Light-responsive elements found in 112 BcbZIP genes. (D) Hormone-responsive elements found in 112 BcbZIP genes. (E) Plant-growth- and development-responsive elements found in 112 BcbZIP genes.
Figure 3. Cis-regulatory elements of BcbZIP genes. (A) Total number of cis-elements found in 112 BcbZIP genes. (B) Stress-responsive elements found in 112 BcbZIP genes. (C) Light-responsive elements found in 112 BcbZIP genes. (D) Hormone-responsive elements found in 112 BcbZIP genes. (E) Plant-growth- and development-responsive elements found in 112 BcbZIP genes.
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Plants 13 01160 g004
Figure 4. Functional enrichment of BcbZIP genes based on gene ontology. (A) GO enrichment analysis of 112 BcbZIP genes showing their involvement in different biological functions. (B) Protein to protein interaction network of BcbZIP genes with ER-stress-responsive genes based on their sequence similarities with Arabidopsis. The co-expression network was generated using a string database. The functional annotation of BcbZIP genes with ER-stress-responsive genes were represented by different colors of nodes showing the shared biological processes, molecular function, and cellular components.
Figure 4. Functional enrichment of BcbZIP genes based on gene ontology. (A) GO enrichment analysis of 112 BcbZIP genes showing their involvement in different biological functions. (B) Protein to protein interaction network of BcbZIP genes with ER-stress-responsive genes based on their sequence similarities with Arabidopsis. The co-expression network was generated using a string database. The functional annotation of BcbZIP genes with ER-stress-responsive genes were represented by different colors of nodes showing the shared biological processes, molecular function, and cellular components.
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Plants 13 01160 g005
Figure 5. The heat map of TPM expression pattern of BcbZIP genes during ER stress (A), cluster analysis of all BcbZIP genes divided into four clusters based on their expression pattern (B). CK: Control, TM: 5 μg/mL, and TT: 25 μg/mL TUDCA application for five days prior to 5 μg/mL TM. Data were recorded after 72 h of TM-induced ER stress.
Figure 5. The heat map of TPM expression pattern of BcbZIP genes during ER stress (A), cluster analysis of all BcbZIP genes divided into four clusters based on their expression pattern (B). CK: Control, TM: 5 μg/mL, and TT: 25 μg/mL TUDCA application for five days prior to 5 μg/mL TM. Data were recorded after 72 h of TM-induced ER stress.
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Plants 13 01160 g006
Figure 6. The nuclear localization of BcbZIP60a and BcbZIP60b investigated in this study.
Figure 6. The nuclear localization of BcbZIP60a and BcbZIP60b investigated in this study.
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Plants 13 01160 g007
Figure 7. The transcriptional activity of BcbZIP60a (A) and BcbZIP60b (B) interacting with BcBiP protein, evaluated using X-α-gal assay in yeast (Scale bar = 50 µm), showing positive activity. The positive and negative controls GAL4 and pGBKT7 empty vector were used, respectively.
Figure 7. The transcriptional activity of BcbZIP60a (A) and BcbZIP60b (B) interacting with BcBiP protein, evaluated using X-α-gal assay in yeast (Scale bar = 50 µm), showing positive activity. The positive and negative controls GAL4 and pGBKT7 empty vector were used, respectively.
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Plants 13 01160 g008
Figure 8. The transcriptional activity of BcbZIP60a (A) and BcbZIP60b (B) interacting with BcBiP protein in N. benthamiana leaf cells on both YNE and YCE terminals.
Figure 8. The transcriptional activity of BcbZIP60a (A) and BcbZIP60b (B) interacting with BcBiP protein in N. benthamiana leaf cells on both YNE and YCE terminals.
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Table 1. Non-synonymous (Ka) and synonymous (Ks) substitution rate and divergence time (MYA) of BcbZIP paralogue gene pairs.
Table 1. Non-synonymous (Ka) and synonymous (Ks) substitution rate and divergence time (MYA) of BcbZIP paralogue gene pairs.
S/No.Paralogue Gene PairsKaKsKa/KsTime (MYA)
1BraC06g036350.1BraC06g036450.10.0027790.0096310.28855600.73
2BraC07g002710.1BraC09g010600.10.0427350.2424910.17623418.48
3BraC03g061850.1BraC08g016590.10.0737270.4224540.17452132.20
4BraC02g023630.1BraC07g027810.10.1328310.4556510.2915234.73
5BraC07g025140.1BraC09g059910.10.0690340.4019450.17174930.64
6BraC01g001260.1BraC03g064330.10.1536180.312790.49112223.84
7BraC02g047730.1BraC02g048410.10.0211650.0397810.5320353.03
8BraC03g007230.1BraC10g025270.10.0906110.2801350.32345621.35
9BraC02g041500.1BraC06g042940.10.0520510.2514050.20704119.16
10BraC02g038580.1BraC06g046020.10.0743680.3544140.20983527.01
11BraC06g009370.1BraC09g068000.10.0729840.2233450.32677917.02
12BraC02g045000.1BraC09g006060.10.1016140.4136330.24566131.53
13BraC02g042590.1BraC06g041080.10.0690650.3196460.21606924.36
14BraC02g044260.1BraC06g038750.10.0895660.2446690.3660718.65
15BraC04g005820.1BraC09g053140.10.2989960.6689320.44697650.99
16BraC07g022530.1BraC09g055620.10.0774060.3371560.22958525.70
17BraC09g055600.1BraC09g055640.10.0016990.011870.1431580.90
18BraC04g031300.1BraC05g002400.10.1104150.2536540.43529619.33
19BraC04g027890.1BraC05g009380.10.0445860.3386050.13167425.81
20BraC06g050540.1BraC10g002520.10.3087321.0589080.29155780.71
21BraC03g039400.1BraC03g039750.10.0174270.0301020.5789332.29
22BraC01g039580.1BraC05g036280.10.0463990.223630.20748117.04
23BraC02g004000.1BraC10g028400.10.0450960.2842740.15863421.67
24BraC09g038170.1BraC09g038420.10.017370.0172921.0045321.32
25BraC02g003360.1BraC10g029390.10.0503060.4247630.11843232.38
26BraC09g001020.1BraC09g007910.10.1723720.354560.48615727.02
27BraC07g026920.1BraC07g041060.10.090980.4840170.18796936.89
28BraC02g002200.1BraC10g031480.10.1195910.9525790.12554472.61
29BraC01g044020.1BraC05g041370.10.0240880.3816760.0631129.09
30BraC06g005390.3BraC09g070850.10.043990.2783650.15802921.22
31BraC03g000260.1BraC03g002970.10.0151990.019310.7871341.47
32BraC07g023180.1BraC09g056730.10.0552460.3829180.14427729.19
33BraC04g017540.2BraC09g063730.10.2133860.5372550.39717940.95
34BraC06g051940.3BraC08g023460.10.1104920.5549960.19908642.30
35BraC05g022350.1BraC08g007780.10.0638070.3487920.18293726.58
36BraC08g034790.1BraC09g071660.10.0642970.4461930.14410234.01
37BraC04g030930.1BraC05g002220.10.0426630.5578690.07647542.52
38BraC08g035030.1BraC10g004690.10.0690880.5932140.11646345.21
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Ayaz, A.; Jalal, A.; Zhang, X.; Khan, K.A.; Hu, C.; Li, Y.; Hou, X. In-Depth Characterization of bZIP Genes in the Context of Endoplasmic Reticulum (ER) Stress in Brassica campestris ssp. chinensis. Plants 2024, 13, 1160. https://doi.org/10.3390/plants13081160

AMA Style

Ayaz A, Jalal A, Zhang X, Khan KA, Hu C, Li Y, Hou X. In-Depth Characterization of bZIP Genes in the Context of Endoplasmic Reticulum (ER) Stress in Brassica campestris ssp. chinensis. Plants. 2024; 13(8):1160. https://doi.org/10.3390/plants13081160

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Ayaz, Aliya, Abdul Jalal, Xiaoli Zhang, Khalid Ali Khan, Chunmei Hu, Ying Li, and Xilin Hou. 2024. "In-Depth Characterization of bZIP Genes in the Context of Endoplasmic Reticulum (ER) Stress in Brassica campestris ssp. chinensis" Plants 13, no. 8: 1160. https://doi.org/10.3390/plants13081160

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