Genome-wide identification and expression analysis of BZR gene family and associated responses to abiotic stresses in cucumber (Cucumis sativus L.)
BMC Plant Biology volume 23, Article number: 214 (2023)
BRASSINAZOLE-RESISTANT (BZR) is a class of specific transcription factor (TFs) involved in brassinosteroid (BR) signal transduction. The regulatory mechanism of target genes mediated by BZR has become one of the key research areas in plant BR signaling networks. However, the functions of the BZR gene family in cucumber have not been well characterized.
In this study, six CsBZR gene family members were identified by analyzing the conserved domain of BES1 N in the cucumber genome. The size of CsBZR proteins ranges from 311 to 698 amino acids and are mostly located in the nucleus. Phylogenetic analysis divided CsBZR genes into three subgroups. The gene structure and conserved domain showed that the BZR genes domain in the same group was conserved. Cis-acting element analysis showed that cucumber BZR genes were mainly involved in hormone response, stress response and growth regulation. The qRT-PCR results also confirmed CsBZR response to hormones and abiotic stress.
Collectively, the CsBZR gene is involved in regulating cucumber growth and development, particularly in hormone response and response to abiotic stress. These findings provide valuable information for understanding the structure and expression patterns of BZR genes.
Brassinosteroids (BRs) are a growth-promoting steroid hormone found in addition to growth hormone (IAA), cytokinin (CTK), ethylene (ETH), gibberellin (GA), and abscisic acid (ABA) . BR plays a vital role in regulating cell germination, cell elongation and division, leaf senescence, photomorphogenesis, pollen tube growth, flowering control, male reproduction, proton pump activity, nucleic acid and protein synthesis, gene expression, photosynthesis and other physiological processes [2–3]. After being accepted by the membrane kinases such as BRISSINOSTEROID INSENSITIVE 1 (BRI1) and BRI1-ASSIMILATED RECEPTOR KINASE1 (BAK1), BR activates the activity of the transcription factor BRI1 EMS SUPPRESSOR 1 (BES1) and its homologous protein BRISINAZOLE RESISTANT1 (BZR1) through signal transduction .
BZR1 and BES1 belong to the same family of transcription factors, which play a key role in the BR signaling pathway in plants. The amino acid sequence similarity of BZR1 and BES1 is 88%, and the sequence consistency of the DNA binding domain is 97% . Yin et al. further confirmed that BES1/BZR1 is a specific class of transcription factors unique to plants and the only transcription factor of the BR signal transduction pathway . The BZR protein contains a nuclear localization sequence (NLS) at the N-terminal, a highly conserved DNA binding domain, a phosphorylation domain (which can be phosphorylated by BRASSINOSTEROID INSENSITIVE2-BIN2), a PEST sequence and a C-terminal domain . BR forms heterodimers by interacting with other regulatory proteins and binds to the BR response element (BRRE) or E-box in the promoter region of the target gene to regulate the expression of downstream BR response genes. Changes in the expression of downstream BR response genes will lead to a series of changes in physiology, biochemistry, growth and development of plants [7, 8]. In Arabidopsis thaliana, 953 BR regulated BZR1 target genes (BRBT) and 1609 potential target genes of BES1 were identified by transcriptional expression profile analysis and chromatin-immunoprecipitation microarray (ChIP) . The activation or inhibition of BZR1 and BES1 on the target gene depends on the binding site or flanking sequence of the target gene promoter .
Currently, 8 BZR/BES gene family members have been identified in Arabidopsis thaliana, 6 in rice, 11 in maize, 15 in Chinese cabbage and 9 in tomato. Further experiments showed that BZR/BES gene family was involved in hormone signal transduction, regulation of growth and development and abiotic stress resistance [6, 11,12,13,14,15,16]. Research on BZR transcription factors in plant species has demonstrated their involvement in the regulation of cell elongation and division, plant morphology, flowering and fertility, quality improvement, and fruit ripening [17,18,19,20,21,22,23,24,25]. Cucumber (Cucumis sativus L.) is an important horticultural crop in the cucurbitaceae plant family, with significant agricultural, biological, and economic value worldwide [26, 27]. China is the largest cucumber producer in the world, accounting for about three quarters of the world’s total output every year . Cucumber fruits are a rich source of various minerals, vitamins, carbohydrates, proteins, and dietary fiber and are also considered a natural antioxidant crop [29, 30]. Despite the known role of the BZR/BES gene family in regulating plant growth and development through BR and other signaling pathways, the function of BZR genes in cucumber has not been reported yet. Therefore, in this study, we analyzed the BZR gene family in cucumber, including its chromosome distribution, gene structure, phylogenetic relationships, conserved sequences, and cis-acting elements. Additionally, we examined the expression pattern of CsBZR gene family members under different hormone and stress treatments. The findings of this study provide crucial information on the function and potential mechanisms of BZR family genes in cucumber.
Identification and characterization of CsBZR gene family
Six candidate genes of CsBZR were identified using AtBES as seed sequence in the cucumber database, the same result was obtained through an online HMM search. Then the existence of the conserved BES1-type domain was verified by CD search and SMART. These 6 CsBZR genes were named CsBZR1 to CsBZR6 according to their location on the chromosome (Fig. 1). The CsBZR genes were distributed on four chromosomes of cucumber. CsBZR1 and CsBZR2 were located on chr01 and chr02, respectively. The chr04 contained CsBZR3 and CsBZR4, while CsBZR5 and CsBZR6 were located at the head and tail of chromosome 6 respectively. It was worth noting that CsBZR3 and CsBZR5 were annotated as β-amylase, the rest were labeled as transcription factors. The predicted sizes of BZR family members in cucumber ranged from 311 to 698 amino acids, and their isoelectric points ranged from 5.78 to 9.71. Subcellular localization prediction showed that all CsBZR genes were located in the nucleus, which was consistent with the function of transcription factors (Table 1).
Phylogenetic tree of BZR genes in cucumber
To further understand the phylogenetic mechanism of CsBZR gene family, the full-length protein sequences of BZR family in cucumber, Arabidopsis, rice, maize and tomato were used to construct phylogenetic trees (Fig. 2). We divided BZR genes into three groups based on their phylogenetic relationship, named Group I to Group III. The AtBZR1 and AtBZR2 as key members and their homologous genes CsBZR2 and CsBZR6 were classified as Group I. Furthermore, OsBZR1 also appeared in Group I, indicating that they were evolutionarily and functionally conservative. Group II contained two members, CsBZR1 and CsBZR4 which belonged to the same subgroup as AtBEH3, AtBEH4, SIBES1.3, SIBES1.4, SIBES1.6, OsBZR2, OsBZR3, OsBZR4, ZmBZR1, ZmBZR2 and ZmBZR11. Members of Group III had long amino acid sequences and were annotated as β-Amylase. The homologous genes of AtBAM7 and AtBAM8 were CsBZR3 and CsBZR5, respectively.
Gene structure and amino acids conserved motif of CsBZR genes
The phylogenetic tree constructed using CsBZR and AtBES1 protein sequences was divided into three groups (Fig. 3A), and the gene structure of the same group was very close. The genes in Group I contained 2–3 CDs and 1–2 introns (red region). All the genes in Group II had only one intron and two exons (yellow region). It was worth noting that the annotation was β-Amylase genes (CsBZR3, CsBZR5, AtBAM7 and AtBAM8) all contain 10 exons, which were much more than other genes.
Highly similar amino acid sequences in functional domains often indicate similar biological functions, thus we explored 10 motifs of BZR proteins (Fig. 3C) in cucumber and Arabidopsis. As shown in Fig. 3B, motif 1 and motif 3 were the most conserved among all the genes. Annotation as β-Amylase genes AtBAM7 in Group III contained motif 1 - motif 10, while the other genes contained other motifs except motif 2, while Group I and Group II only contained motif 1, motif 3 and motif 2. The same subgroup consists of almost the same conserved motifs, indicating that they may have similar functions.
Collinearity analysis of BZR family genes in cucumber
No collinear gene pairs were found in cucumber species, while there were more collinear gene pairs in tomato and cucumber than in Arabidopsis and cucumber. Collinearity analysis showed that CsBZR6 had collinear gene pairs with AtBZR1, AtBEH1, and AtBEH2 in Arabidopsis and cucumber (Fig. 4A). All CsBZR genes were found to have a collinear relationship with SlBZR genes, resulting in a total of 10 pairs (Fig. 4B). These results illustrated that the genetic relationship between CsBZR genes and SlBZR genes was close.
Analysis of cis acting elements in CsBZR genes
Cis-element prediction can help further understand the potential regulatory mechanism of CsBZR genes. The upstream promoter region of cucumber BZR family genes contained many cis-elements (Fig. 5), that could respond to plant hormones, abiotic stresses and plant development-related (Table 2). Among these cis-elements, ABRE, AuxRR-core, CGTCA-motif, P-box, TATC-box, TGACG-motif and TCA-element were involved in abscisic acid, auxin, methyl jasmonate, gibberellin and salicylic acid responsiveness, respectively. In addition, CsBZR genes were also involved in low-temperature, drought and meristem expression. These results indicated that CsBZR family genes may be involved in variety of stress and plant hormone response processes, which could effectively promote plant growth and stress resistance, as well as have important biological functions.
Tissue specific expression pattern of CsBZR genes
In order to explore the expression of CsBZR gene in different tissues of cucumber, we downloaded relevant data from cucumber genome website and used TBtools software to create an expression pattern heat map. As shown in Fig. 6, CsBZR6 was widely expressed in all tissues and organs and showed high expression levels, indicating that CsBZR6 played a vital role in cucumber tissue development. Conversely, the expression levels of CsBZR5 were low in all tissues. The expression level of CsBZR4 in ovary_fertilized, ovary, ovary_unfertilized and roots was also at a high level, while was the low expression in tendril_base and tendril.
Expression profiles of CsBZR genes in response to plant hormone
BZR transcription factors are usually reported to be involved in plant growth and development. The indole-3-acetic acid (IAA), Gibberellin A3 (GA3), Abscisic Acid (ABA), ethephon (ETH), epi-brassinolide (EBL) were used to detect the response of CsBZR genes. As shown in Fig. 7, all CsBZR genes significantly responded to IAA, with the relative expression of CsBZR3 and CsBZR6 at 12 h being 20-fold higher than at 0 h. With the exception of CsBZR4 and CsBZR5, the response of the other CsBZR genes to GA3 was over four times greater. CsBZR3 showed the most significant response to ETH, with a relative expression of 26-fold greater than at 0 h, while the relative expression of other CsBZR genes ranged from 2 to 7. CsBZR genes also significantly responded to EBL, with the relative expression of CsBZR1, 2, and 3 being 9, 13, and 11-fold greater than at 0 h, respectively. Similar to EBL treatment, ABA induced up-regulation of all CsBZR genes, with relative expression multiples of 51, 10, 16, 5, 5, and 10 times, respectively. Overall, these results suggested that CsBZR genes may be involved in various hormone regulations in a complex manner, and the crosstalk between this family and plant hormones needs to be explored in detail.
Expression profiles of CsBZR genes in response to abiotic stress
In order to explore the response of CsBZR genes to abiotic stress, we verified their expression patterns under heavy metals, drought, salt and low temperature. As shown in Fig. 8, the relative expressions of CsBZR4 and CsBZR5 under Cd stress were low, ranging from 2 to 3, while the relative expressions of CsBZR1, CsBZR2, CsBZR3 and CsBZR6 were high, which were 4, 5, 16 and 5 folds higher than that of 0 h, respectively. Under 20% PEG treatment, the relative expression of all CsBZR genes was greater than 3, and the responses of CsBZR3 and CsBZR6 were particularly significant, reaching 13.9 and 19.3. Salt stress induced up regulation of all CsBZR genes, in which CsBZR1, 2, 3 had a high expression. The response expression of CsBZR1, 2, 3, 4 to low temperature stress was higher than 4, while the response expression of CsBZR5, 6 was lower than 3. The above results showed that CsBZR genes could respond to a variety of abiotic stresses and were up-regulated.
BZR protein is an important class of transcription factors in plants, and it is also a key component of BR signal transduction pathway. BZR protein not only regulates plant growth and development, but also participates in the response of many plants to abiotic stress [15, 31,32,33,34]. Since the BZR gene family of Arabidopsis thaliana was excavated, BZR gene family of many other species have also been identified, including Brassica rapa 、Beta vulgaris 、Zea mays 、Triticum aestivum  and tomato . Characterization and systematic analysis of BZRs in cucumber have not been completed to date. In this study, we identified the members of cucumber BZR family, and analyzed the physical and chemical properties of the protein, gene structure, conservation, cis-elements and related expression patterns.
Six BZR family genes were identified from the whole genome of cucumber (Table 1). The number of cucumber BZR family members is two less than that of Arabidopsis and three less than that of tomato . In addition to the 6 BZR genes initially discovered in Arabidopsis, it was later discovered that BAM7 and BAM8 in the BAM family also have a BRASSINAZOLE RESISTANT1 (BZR1) type DNA binding domain, which can also be found in transcription factors that mediate the brassinosteroid (BR) response . In order to better understand the evolutionary relationship among BZR family members in different species, we constructed a phylogenetic tree with BZR proteins from cucumber, Arabidopsis, tomato, maize and rice. Phylogenetic analysis showed that CsBZR genes were divided into three subfamilies. The first subgroup included AtBZR1 and OsBZR1, and CsBZR2 and CsBZR6 belong to the same group. The second subgroup contained CsBZR1 and CsBZR4, which are close to the branches of SiBES1.3, SiBES1.4 and SiBES1.6. The third subgroup contained CsBZR3 and CsBZR5, which are annotated as starch hydrolases together with AtBAM7 and AtBAM8. Tandem repeat and fragment replication is the main ways of gene family replication, and participate in the formation and functional differentiation of new genes . In our study, there was no collinear relationship between cucumber BZR genes, while CsBZR6 and AtBZR1, AtBEH1 and AtBEH2 had collinearity. All cucumber BZR genes and tomato BZR genes form collinear pairs, indicating that they are more closely related genetically.
In terms of gene structure and conserved motifs, the classification of Arabidopsis and cucumber is similar to that of the evolutionary tree. CsBZR3, CsBZR5, AtBAM7 and AtBAM8 annotated as starch hydrolases were divided into the same group, and there were significant differences in structure and conserved motifs from other BZR genes. In Arabidopsis, BAM7 and BAM8 have a BAM-like domain. In addition to the function of normal BZR protein, BZR1-BAMS can regulate many genes responding to BRs, and also regulate by binding the ligands in the BAM-like domain to transmit metabolic signals, plant growth and development can be controlled by crosstalk with BR signals [37, 39]. Compared to other BZR genes, CsBZR3 and CsBZR5 have a greater number of introns, exons and conserved motifs diversity, suggesting that they may have additional functions, such as involvement in amylase hydrolysis. These results showed that most BZR genes come from the same ancestor and their functions are conserved.
Cis-acting elements are noncoding DNA sequences that exist in the promoter region and participate in the regulation of gene expression. In this study, we selected 12 elements and divided them into three categories (hormone response, stress response and plant development response). Hormone response included responses to ABA, IAA, MeJA, gibberellin and salicylic acid. Stress responses included low-temperature, drought-inducibility and defense and stress responsiveness. Plant development included light responsive elements, zein metabolism regulation and meristem expression. Some reports also confirmed that the BZR family is involved in a variety of hormone signaling pathways [40,41,42], stress response [15, 43,44,45], and plant growth regulation [19, 46, 47].
BZR family genes are specifically expressed in different tissues and organs of many plants [14, 16, 44]. In Arabidopsis, the transcriptional expression level of BZR gene was higher in roots and buds, but lower in stems, fruits and flowers [48, 49]. The expression level of BZR family genes was high in maize seedlings and endosperm . SlBZR02 and SlBZR09 genes in tomato are generally expressed in most tissues, and their expression levels are very high, while other SlBZR genes are only highly expressed in some tissues . We used the published cucumber transcriptome data to analyze the expression pattern of CsBZR genes in different tissues (root, stem, leaf, female, male, ovary_fertilized, ovary_unfertilized, tendril_base and tendril). CsBZR6 was highly expressed in almost all tissues, while the transcriptional level of CsBZR5 was relatively low. The remaining CsBZR1, 2, 3 and 4 have a considerable transcriptional level in different tissues. Therefore, the differential expressions of CsBZR family members in different tissues indicate that they play a regulatory role in the growth and development of cucumber, and there is functional redundancy.
A large number of studies have shown that BZR gene is involved in the response to various signals, including IAA, ABA, GA, ETH, NaCl and drought stress [31, 42, 44, 50,51,52]. In the current study, we identified three major types of acting elements: hormone response, stress response and plant development response. The hormone response elements included ABA, IAA, methyl jasmonate, GA and salicylic acid responsiveness. The plant hormone response pattern verified that CsBZR family genes could be up-regulated at a variety of hormone levels, especially under ABA, ETH and EBR treatments (Fig. 7). BZR as a key transcription factor in BR signal transduction is involved in regulating multiple stress responses. Cis-acting element analysis showed that CsBZR genes were associated with low-temperature and drought. Under low-temperature treatment, the expression of CsBZR1, 3 and 4 were more than 4 folds compared to 0 h, while CsBZR3, 4, 5 and 6 were significantly up-regulated under 20% PEG treatment. Studies in Arabidopsis showed that continuous low temperature treatment could accumulate dephosphorylated BZR1, and the frost resistance of functional acquired mutants of BZR1 and BES1 was significantly enhanced . In Chinese cabbage, BrBZR1-1, BrBES1-3, BrBEH4, BrBEH6, BrBEH7 and BrBEH8 showed obvious responses to cold. These BrBZR transcription factors were considered to be the transcriptional activators of CBF cold response pathway in Chinese cabbage . The findings of Ye et al. proved that the members of BES/BZR family in Arabidopsis played a role in response to drought stress. BES1 protein could directly and negatively regulate the expression of drought response gene RD26, thus mediating the signal cross between BR and drought pathway . In wheat, the BES/BZR family transcription factor TaBZR2 plays an active role in drought response and reduces the accumulation of reactive oxygen species by activating TaGST1 . Surprisingly CsBZR6 was very active in the expression pattern in different tissues, while the expression was relatively low in hormone-induced and drought stresses. This could be because CsBZR6 was closely related to cucumber growth and development but was insensitive to hormone treatment and drought stress. CsBZR family genes responded significantly to salt stress, especially the expression of CsBZR1, 2 and 3 was more than 20-folds that of the 0 h. Similar results were also reported in maize and Eucalyptus grandis [14, 54]. In this study, we also analyzed the expression pattern of CsBZR genes under cadmium stress. Except CsBZR4 and CsBZR5, the expression of other genes had a high level. Many studies have shown that BR can alleviate heavy metal stress and improve plant tolerance [55,56,57]. BZR, as the only transcription factor in BR signal, may have a potential regulatory effect under heavy metal stress. These findings reveal the complexity of cucumber BZR genes regulation and establish the foundation for further study on the function of the cucumber BZR genes.
In this study, six cucumber BZR genes were identified, which were divided into three branches according to the systematic evolutionary tree. As key transcription factors in the BR signaling pathway, CsBZRs were involved in hormone and stress responses as well as growth regulation in cucumber. Tissue expression patterns showed that CsBZR6 was highly expressed in various cucumber tissues and may be an important gene regulating cucumber growth and development. CsBZRs responded to hormone induction, particularly CsBZR3 and CsBZR6. CsBZRs also participated in the regulation of abiotic stress, with CsBZR1, CsBZR2 and CsBZR3 showing significant responses to most stresses. These findings provide a reference for the future research on the function of CsBZR genes and the exploration of potential regulatory network.
Materials and methods
Plant material culture
Cucumber seeds (Cucumis sativus L., ‘xinchun 4’) were procured from the Gansu Academy of Agricultural Sciences, China. The seeds were kept in a dark environment at a temperature of 28℃ for the purpose of germination. After successful germination, the incubator conditions were adjusted to maintain a temperature of 25℃/18℃, with a photoperiod of 14/10 h, to ensure optimal growth of the seedlings.
Following 7 d of cultivation, the seedlings were transplanted into a plastic box containing the Yamazaki nutrient solution, for further cultivation. Based on the growth rate of the cucumber seedlings, the Yamazaki nutrient solution was varied in concentration, ranging from 1/8, 1/6, 1/4, 1/2, to 1. Subsequently, the seedlings were subjected to different treatments after 20 d of growth.
Identification of BZR genes in cucumber
We performed a BLASTP search using the BZR gene family from Arabidopsis (https://www.arabidopsis.org/) in the cucumber genome database (http://www.cucurbitgenomics.org/) with an e-value of 10− 10. In addition, we downloaded the BES1 domain file (PF05687) from the Pfam website (http://pfam.xfam.org/) and uploaded it to the HMM website (https://www.ebi.ac.uk/Tools/hmmer/search/hmmsearch) to search for potential genes in the cucumber genome containing this conserved domain . Duplicate genes were removed by comparing the results of the two different searches. The remaining genes were further validated for the presence of the BES1-type domain using the CD search website and the SMART website (http://smart.embl-heidelberg.de/). The CsBZR gene and protein sequence information can be found in Supplementary Material 1.
Chromosome distribution Bioinformatic analyses of BZR gene family in cucumber
The position information of CsBZR family genes was retrieved from the cucumber genome database, and the distribution of genes on chromosomes was visualized using an online website (http://www.mg2c.iask.in/mg2c_v2.0/). The secondary structure and subcellular localization of the protein sequences were predicted using the ExPASy online website (https://web.expasy.org/protparam/)..
Construction of phylogenetic tree and collinearity analysis
The phylogenetic tree of BZR gene family of cucumber, A. thaliana, tomato, corn, and rice were constructed by using MEGA 7 software with MUSCLE methods to align multiple sequences and bootstrapping was performed 1000 times to obtain self-expanding values for each branch in Fig. . Finally, the neighbor-joining is selected to represent their evolutionary relationship and beautify the constructed tree by the EvolView website. See supplementary material 2 for registration numbers of various species.
McScanX was utilized to search for homology by comparing the protein-coding genes from the cucumber genome against the genomes of Arabidopsis and tomato using BLASTP, with a retrieval threshold set at E-value < E− 5. Default parameters were used for all other settings. Whole-genome BLASTP results were used to compute collinear blocks for all possible pairs of chromosomes and scaffolds . Subsequently, TBtools was used to visualize the identified collinear pairs of cucumber, Arabidopsis and tomato .
Gene structure and conservative motif analysis
To analyze conservative motifs, the protein sequences of CsBZR and AtBZR were uploaded to the MEME website (http://meme-suite.org/tools/meme). The maximum number of motifs was set to 10, and all other parameters were set to their default values .
Analysis of cis-acting elements in CsBZR gene promoters
TBtools software intercepted a 2000 bp region upstream of the start codon of CsBZR family genes as a promoter, and then the cis acting elements are predicted through PlantCare website (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/) .
Expression patterns of BZR gene family in different tissues of cucumber
CsBZR transcriptome data (FPKM) was downloaded from cucumber genome database (http://www.cucurbitgenomics.org/rnaseq/cu/3, BioProject PRJNA80169). Transcriptome data were normalized by logarithms, and then expression heat map were drawn using TBtools software. The color scale indicates the level of gene expression .
Hormone and abiotic stress treatments
The expression pattern experiment was divided into hormone and abiotic stress treatments. To prepare the treatment concentrations, ABA, IAA, GA, and ETH were dissolved in 100 mL distilled water to a concentration of 1 mM, and then diluted accordingly. EBL was dissolved in 100 mL 90% ethanol solution to a concentration of 1 mM, and then diluted to the treatment concentration. Hormone treatments involved the application of ABA (100 µM), IAA (20 µM), GA (20 µM), EBL (0.5 µM), and ETH (20 µM). Samples were collected at 0, 6, 12, and 24 h post-treatment, and untreated seedlings from the same batch were used as controls. At each time point, three biological replicates were collected, with each replicate consisting of three independent seedlings.
Drought, low temperature, CdCl2 and salt were set as abiotic stress treatment. All reagents are purchased from Shanghai MACKLIN Co., Ltd. Add PEG 6000, CdCl2 and NaCl into 1 L nutrient solution to prepare 20% PEG 6000, 200 µM CdCl2 and 200 mM NaCl solution, respectively. The low temperature stress was set at 12℃/8℃. Samples were collected after treatment for 0, 6, 12 and 24 h respectively. Normal growth seedlings were used as control. Three individual seedlings were collected for one repetition and three biological replicates were collected at each time point.
RNA isolation, cDNA synthesis and quantitative real-time PCR analysis
Total RNA was extracted using the DP432 kit (Tiangen, China) following the manufacturer’s instructions. cDNA was synthesized using the fastking cDNA dispersion RT supermax kit (Tiangen, China) with 2 µL of RNA as the template. The SYBR Green kit (Tiangen, China) was used for the fluorescence quantitative system. Primers were synthesized by Shanghai Shenggong Company. The reaction system volume was 20 µL, which contained 2 µL of cDNA solution, 10 µL of 2*SuperReal PreMix Plus, 0.6 µL of 10 µM forward and reverse primers, 0.4 µL of 50*ROX Reference Dye, and 6.4 µL of distilled deionized water. qRT-PCR analysis was performed using the LightCycler® 480 II real-time fluorescence quantitative PCR instrument. The reference gene used was Actin3 (DQ115883). The relative level of gene expression was analyzed using the 2−∆∆Ct method. See supplementary material 3 for primers information.
The qRT-PCR data supporting the gene relative expression results of this study can be found in supplementary material 4. The login numbers of all CsBZR genes identifed and tissue specific expression transcriptome data of CsBZR genes (BioProject PRJNA80169) can be obtained in the cucumber genome database (http://www.cucurbitgenomics.org).
BRI1-ASSIMILATED RECEPTOR KINASE1
N-terminal nuclear localization sequence
Nolan T, Chen J, Yin Y. Cross-talk of Brassinosteroid signaling in controlling growth and stress responses. Biochem J. 2017;474(16):2641–61.
Yang C-J, Zhang C, Lu Y-N, Jin J-Q, Wang X-L. The mechanisms of brassinosteroids’ action: from signal transduction to plant development. Mol Plant. 2011;4(4):588–600.
Clouse SD. Brassinosteroid signal transduction: from receptor kinase activation to transcriptional networks regulating plant development. Plant Cell. 2011;23(4):1219–30.
Belkhadir Y, Jaillais Y. The molecular circuitry of brassinosteroid signaling. New Phytol. 2015;206(2):522–40.
Wang Z-Y, Nakano T, Gendron J, He J, Chen M, Vafeados D, Yang Y, Fujioka S, Yoshida S, Asami T. Nuclear-localized BZR1 mediates brassinosteroid-induced growth and feedback suppression of brassinosteroid biosynthesis. Dev Cell. 2002;2(4):505–13.
Yin Y, Vafeados D, Tao Y, Yoshida S, Asami T, Chory J. A new class of transcription factors mediates brassinosteroid-regulated gene expression in Arabidopsis. Cell. 2005;120(2):249–59.
Tang W, Yuan M, Wang R, Yang Y, Wang C, Oses-Prieto JA, Kim T-W, Zhou H-W, Deng Z, Gampala SS. PP2A activates brassinosteroid-responsive gene expression and plant growth by dephosphorylating BZR1. Nat Cell Biol. 2011;13(2):124–31.
Zhao J, Peng P, Schmitz RJ, Decker AD, Tax FE, Li J. Two putative BIN2 substrates are nuclear components of brassinosteroid signaling. Plant Physiol. 2002;130(3):1221–9.
Yu X, Li L, Zola J, Aluru M, Ye H, Foudree A, Guo H, Anderson S, Aluru S, Liu P. A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana. Plant J. 2011;65(4):634–46.
Sun Y, Fan X-Y, Cao D-M, Tang W, He K, Zhu J-Y, He J-X, Bai M-Y, Zhu S, Oh E. Integration of brassinosteroid signal transduction with the transcription network for plant growth regulation in Arabidopsis. Dev Cell. 2010;19(5):765–77.
Chen L-G, Gao Z, Zhao Z, Liu X, Li Y, Zhang Y, Liu X, Sun Y, Tang W. BZR1 family transcription factors function redundantly and indispensably in BR signaling but exhibit BRI1-independent function in regulating anther development in Arabidopsis. Mol Plant. 2019;12(10):1408–15.
Su D, Xiang W, Wen L, Lu W, Shi Y, Liu Y, Li Z. Genome-wide identification, characterization and expression analysis of BES1 gene family in tomato. BMC Plant Biol. 2021;21(1):1–17.
Bai M-Y, Zhang L-Y, Gampala SS, Zhu S-W, Song W-Y, Chong K, Wang Z-Y. (2007) Functions of OsBZR1 and 14-3-3 proteins in brassinosteroid signaling in rice. Proceedings of the National Academy of Sciences 104 (34):13839–13844
Manoli A, Trevisan S, Quaggiotti S, Varotto S. Identification and characterization of the BZR transcription factor family and its expression in response to abiotic stresses in Zea mays L. Plant Growth Regul. 2018;84(3):423–36.
Saha G, Park J-I, Jung H-J, Ahmed NU, Kayum MA, Kang J-G, Nou I-S. Molecular characterization of BZR transcription factor family and abiotic stress induced expression profiling in Brassica rapa. Plant Physiol Biochem. 2015;92:92–104.
Wang B, Zhu X, Wei X. (2021) Genome-wide identification, structural analysis, and expression profiles of the BZR gene family in tomato.Journal of Plant Biochemistry and Biotechnology:1–12
Park CH, Kim T-W, Son S-H, Hwang J-Y, Lee SC, Chang SC, Kim S-H, Kim SW, Kim S-K. Brassinosteroids control AtEXPA5 gene expression in Arabidopsis thaliana. Phytochemistry. 2010;71(4):380–7.
Chaiwanon J, Wang Z-Y. Spatiotemporal brassinosteroid signaling and antagonism with auxin pattern stem cell dynamics in Arabidopsis roots. Curr Biol. 2015;25(8):1031–42.
Li Q-F, He J-X. BZR1 interacts with HY5 to mediate brassinosteroid-and light-regulated cotyledon opening in Arabidopsis in darkness. Mol Plant. 2016;9(1):113–25.
Tong H, Jin Y, Liu W, Li F, Fang J, Yin Y, Qian Q, Zhu L, Chu C. DWARF AND LOW-TILLERING, a new member of the GRAS family, plays positive roles in brassinosteroid signaling in rice. Plant J. 2009;58(5):803–16.
Fang Z, Ji Y, Hu J, Guo R, Sun S, Wang X. Strigolactones and brassinosteroids antagonistically regulate the stability of the D53–OsBZR1 complex to determine FC1 expression in rice tillering. Mol Plant. 2020;13(4):586–97.
Domagalska MA, Schomburg FM, Amasino RM, Vierstra RD, Nagy F, Davis SJ. (2007) Attenuation of brassinosteroid signaling enhances FLC expression and delays flowering.
Ye Q, Zhu W, Li L, Zhang S, Yin Y, Ma H, Wang X. (2010) Brassinosteroids control male fertility by regulating the expression of key genes involved in Arabidopsis anther and pollen development. Proceedings of the National Academy of Sciences 107 (13):6100–6105
Liu L, Jia C, Zhang M, Chen D, Chen S, Guo R, Guo D, Wang Q. Ectopic expression of a BZR-1D transcription factor in brassinosteroid signalling enhances carotenoid accumulation and fruit quality attributes in tomato. Plant Biotechnol J. 2014;12(1):105–15.
Guo Yf, Shan W, Liang Sm Wu, Cj, Wei W, Chen Jy Lu, Wj K Jf. MaBZR1/2 act as transcriptional repressors of ethylene biosynthetic genes in banana fruit. Physiol Plant. 2019;165(3):555–68.
Pan Y, Qu S, Bo K, Gao M, Haider KR, Weng Y. QTL mapping of domestication and diversifying selection related traits in round-fruited semi-wild Xishuangbanna cucumber (Cucumis sativus L. var. Xishuangbannanesis). Theor Appl Genet. 2017;130(7):1531–48.
Che G, Zhang X. Molecular basis of cucumber fruit domestication. Curr Opin Plant Biol. 2019;47:38–46.
Gebretsadik K, Qiu X, Dong S, Miao H, Bo K. Molecular research progress and improvement approach of fruit quality traits in cucumber. Theor Appl Genet. 2021;134(11):3535–52.
Cortbaoui PE, Ngadi MO. (2015) New method to quantify postharvest quality loss of cucumber using the Taguchi approach.
Mostafa YS, Hashem M, Alshehri AM, Alamri S, Eid EM, Ziedan E-SH, Alrumman SA. Effective management of Cucumber Powdery Mildew with essential oils. Agriculture. 2021;11(11):1177.
Sun F, Yu H, Qu J, Cao Y, Ding L, Feng W, Khalid MHB, Li W, Fu F. Maize ZmBES1/BZR1-5 decreases ABA sensitivity and confers tolerance to osmotic stress in transgenic Arabidopsis. Int J Mol Sci. 2020;21(3):996.
Liao K, Peng Y-J, Yuan L-B, Dai Y-S, Chen Q-F, Yu L-J, Bai M-Y, Zhang W-Q, Xie L-J, Xiao S. Brassinosteroids antagonize jasmonate-activated plant defense responses through BRI1-EMS-SUPPRESSOR1 (BES1). Plant Physiol. 2020;182(2):1066–82.
Song X, Ma X, Li C, Hu J, Yang Q, Wang T, Wang L, Wang J, Guo D, Ge W. Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species. BMC Genomics. 2018;19(1):1–15.
Yin Y, Qin K, Song X, Zhang Q, Zhou Y, Xia X, Yu J. BZR1 transcription factor regulates heat stress tolerance through FERONIA receptor-like kinase-mediated reactive oxygen species signaling in tomato. Plant Cell Physiol. 2018;59(11):2239–54.
Wang W, Sun Y-Q, Li G-L, Zhang S-Y. Genome-wide identification, characterization, and expression patterns of the BZR transcription factor family in sugar beet (Beta vulgaris L). BMC Plant Biol. 2019;19(1):1–12.
Kesawat MS, Kherawat BS, Singh A, Dey P, Kabi M, Debnath D, Saha D, Khandual A, Rout S, Ali A. Genome-wide identification and characterization of the brassinazole-resistant (BZR) gene family and its expression in the various developmental stage and stress conditions in wheat (Triticum aestivum L). Int J Mol Sci. 2021;22(16):8743.
Reinhold H, Soyk S, Šimková K, Hostettler C, Marafino J, Mainiero S, Vaughan CK, Monroe JD, Zeeman SC. β-Amylase–like proteins function as transcription factors in Arabidopsis, controlling shoot growth and development. Plant Cell. 2011;23(4):1391–403.
Panchy N, Lehti-Shiu M, Shiu S-H. Evolution of gene duplication in plants. Plant Physiol. 2016;171(4):2294–316.
Soyk S, Šimková K, Zürcher E, Luginbühl L, Brand LH, Vaughan CK, Wanke D, Zeeman SC. The enzyme-like domain of Arabidopsis nuclear β-amylases is critical for DNA sequence recognition and transcriptional activation. Plant Cell. 2014;26(4):1746–63.
Zhao X, Dou L, Gong Z, Wang X, Mao T. BES 1 hinders ABSCISIC ACID INSENSITIVE 5 and promotes seed germination in Arabidopsis. New Phytol. 2019;221(2):908–18.
Li Q, Xu F, Chen Z, Teng Z, Sun K, Li X, Yu J, Zhang G, Liang Y, Huang X. Synergistic interplay of ABA and BR signal in regulating plant growth and adaptation. Nat Plants. 2021;7(8):1108–18.
Zhong C, Patra B, Tang Y, Li X, Yuan L, Wang X. A transcriptional hub integrating gibberellin–brassinosteroid signals to promote seed germination in Arabidopsis. J Exp Bot. 2021;72(13):4708–20.
Li Y, He L, Li J, Chen J, Liu C. Genome-wide identification, characterization, and expression profiling of the legume BZR transcription factor gene family. Front Plant Sci. 2018;9:1332.
Cui X-Y, Gao Y, Guo J, Yu T-F, Zheng W-J, Liu Y-W, Chen J, Xu Z-S, Ma Y-Z. BES/BZR transcription factor TaBZR2 positively regulates drought responses by activation of TaGST1. Plant Physiol. 2019;180(1):605–20.
Li H, Ye K, Shi Y, Cheng J, Zhang X, Yang S. BZR1 positively regulates freezing tolerance via CBF-dependent and CBF-independent pathways in Arabidopsis. Mol Plant. 2017;10(4):545–59.
Lachowiec J, Mason GA, Schultz K, Queitsch C. Redundancy, feedback, and robustness in the Arabidopsis thaliana BZR/BEH gene family. Front Genet. 2018;9:523.
Xia X, Dong H, Yin Y, Song X, Gu X, Sang K, Zhou J, Shi K, Zhou Y, Foyer CH. Brassinosteroid signaling integrates multiple pathways to release apical dominance in tomato. Proceedings of the National Academy of Sciences. 2021;118(11):e2004384118
Yin Y, Wang Z-Y, Mora-Garcia S, Li J, Yoshida S, Asami T, Chory J. BES1 accumulates in the nucleus in response to brassinosteroids to regulate gene expression and promote stem elongation. Cell. 2002;109(2):181–91.
He J-X, Gendron JM, Sun Y, Gampala SS, Gendron N, Sun CQ, Wang Z-Y. BZR1 is a transcriptional repressor with dual roles in brassinosteroid homeostasis and growth responses. Science. 2005;307(5715):1634–8.
Walcher CL, Nemhauser JL. Bipartite promoter element required for auxin response. Plant Physiol. 2012;158(1):273–82.
Su Q, Zheng X, Tian Y, Wang C. Exogenous brassinolide alleviates salt stress in Malus hupehensis Rehd. By regulating the transcription of NHX-Type Na+ (K+)/H+ antiporters. Front Plant Sci. 2020;11:38.
He Y, Liu H, Li H, Jin M, Wang X, Yin X, Zhu Q, Rao J. Transcription factors DkBZR1/2 regulate cell wall degradation genes and ethylene biosynthesis genes during persimmon fruit ripening. J Exp Bot. 2021;72(18):6437–46.
Ye H, Liu S, Tang B, Chen J, Xie Z, Nolan TM, Jiang H, Guo H, Lin H-Y, Li L. RD26 mediates crosstalk between drought and brassinosteroid signalling pathways. Nat Commun. 2017;8(1):1–13.
Fan C, Guo G, Yan H, Qiu Z, Liu Q, Zeng B. Characterization of Brassinazole resistant (BZR) gene family and stress induced expression in Eucalyptus grandis. Physiol Mol Biology Plants. 2018;24(5):821–31.
Hussain A, Nazir F, Fariduddin Q. 24-epibrassinolide and spermidine alleviate mn stress via the modulation of root morphology, stomatal behavior, photosynthetic attributes and antioxidant defense in Brassica juncea. Physiol Mol Biology Plants. 2019;25(4):905–19.
Jan S, Alyemeni MN, Wijaya L, Alam P, Siddique KH, Ahmad P. Interactive effect of 24-epibrassinolide and silicon alleviates cadmium stress via the modulation of antioxidant defense and glyoxalase systems and macronutrient content in Pisum sativum L. seedlings. BMC Plant Biol. 2018;18(1):1–18.
Jakubowska D, Janicka M. The role of brassinosteroids in the regulation of the plasma membrane H+-ATPase and NADPH oxidase under cadmium stress. Plant Sci. 2017;264:37–47.
Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011;39(suppl2):W29–W37.
Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, De Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res. 2012;40(W1):W597–W603.
Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870–4.
Wang Y, Tang H, DeBarry JD, Tan X, Li J, Wang X, Lee T-h, Jin H, Marler B, Guo H. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012;40(7):e49–9.
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, Xia R. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020;13(8):1194–202.
Hu B, Jin J, Guo A-Y, Zhang H, Luo J, Gao G. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 2015;31(8):1296–7.
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37(suppl2):W202–8.
Lescot M, D?hais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouz? P, Rombauts S: PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic acids research 2002, 30(1):325–327.
Li Z, Zhang Z, Yan P, Huang S, Fei Z, Lin K. RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics. 2011;12(1):1–11.
This experiment thanks the support and help of the Key Laboratory of Aridland Crop Science, China.
This research was supported by Research Program Sponsored by the State Key Laboratory of Aridland Crop Science of China (GSCS-2021-09); “Double first-class” key scientific research project of Gansu Education Department (GSSYLXM-02); Special project of the central government to guide local scientific and Technological Development (ZCYD-2021-5); Natural Science Foundation of Gansu Province (21JR7RA816).
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There are no ethical issues involved in this paper. The cucumber cultivar (Cucumis sativus L. cv. Xinchun No. 4) seed used in this research was produced by Xintai-Kerun Seed Industry Co. Ltd., Shandong, China. Plant sampling and use in accordance with applicable laws and statements.
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Luo, S., Zhang, G., Zhang, Z. et al. Genome-wide identification and expression analysis of BZR gene family and associated responses to abiotic stresses in cucumber (Cucumis sativus L.). BMC Plant Biol 23, 214 (2023). https://doi.org/10.1186/s12870-023-04216-9