Genome-wide characterization of bZIP transcription factors and their expression patterns in response to drought and salinity stress in Jatropha curcas
Introduction
Transcription factors (TFs) are proteins that regulate gene expression by binding to gene regulatory regions and play an important role in governing many vital growth and developmental processes [1]. The basic leucine (Leu) zipper (bZIP) family is one of the largest families of TFs and comprises a group of conserved transcriptional regulators that are widely distributed in eukaryotes including plants [2]. bZIP proteins are characterized by a conserved 40–80 amino acid (aa) bZIP domain that includes a basic region and an adjacent leucine zipper region [3,4]. Specifically, the basic region has an N-x7-R/K motif that binds to specific sequences within the promoter regions of DNA. This motif preferentially binds to DNA sequences containing core ACGT cis-acting elements such as A-box (TACGTA), C-box (GACGTC) and G-box (CACGTG) elements [2,5,6]. In addition, the Leu zipper region contains heptad repeats (x9-L-x6-L-x6-L) of Leu or isoleucine (Ile), valine (Val), phenylalanine (Phe), or methionine (Met) and forms an amphiphilic α-helix that regulates dimerization before bZIP proteins bind DNA [2]. The complex interactions between bZIP TFs and cis-acting elements could activate, enhance or inhibit transcription and thereby regulate the expression of corresponding downstream genes [2].
bZIP genes have been found to regulate many important biological processes, including flower and vascular tissue development [7,8], organ and tissue differentiation [9], embryogenesis [10], seed maturation and regulation of the expression of genes that encode storage proteins [11]. Moreover, bZIP TFs have a very typical function and are also involved in responses to a variety of abiotic/biotic stresses such as high salinity, drought, heat stress, cold stress and pathogen infection [[12], [13], [14], [15]]. Drought stress and salt stress seriously impact the growth and quality of industrial crops. The function of many bZIP genes to resist drought stress and salt stress has been identified in many plants. For example, in Arabidopsis (Arabidopsis thaliana L.), AtbZIP17 and AtbZIP60 could enhance the salt tolerance under salinity stress [3,16], and AtbZIP1 is expressed in response to abiotic stresses such as drought and high-salinity stress [17]. In rice (Oryza sativa L.), OsbZIP62 is involved in the abscisic acid (ABA) signaling pathway and positively regulates the resistance to drought by upregulating the expression of drought tolerance-related genes [18], and OsbZIP23 contributes strongly to reduced plant sensitivity to ABA, thus improving the ability to withstand drought and salinity stress [19]. In soybean (Glycine max L.), GmbZIP44 and GmbZIP110 are negative regulators of ABA signaling and provide resistance to salinity stress [20,21]. Similarly, in castor bean (Ricinus communis L.), RcbZIPs 2, 9, 22 and 36 may be involved in the regulation of resistance to drought stress [22]. With the rapid development of high-throughput sequencing technology, the different methods available for identifying TFs on the basis of genomic information have rapidly increased in abundance. To date, previous studies have reveled 75 bZIP genes in Arabidopsis [2], 89 bZIPs in rice [14], 88 bZIPs in Populus trichocarpa [23], 92 bZIPs in sorghum (Sorghum bicolor (L.) Moench) [24], 125 bZIPs in maize (Zea mays L.) [25], 55 bZIPs in grape (Vitis vinifera L.) [26], 49 bZIPs in castor bean [22] and so forth.
Jatropha curcas L. is considered as a biodiesel plant with oil-rich seeds and rapid growth [27,28]. Notably, J. curcas is adaptable to dry climates and high-salt soil environments [27,29]. Drought and soil salinity are the major abiotic stresses that influence both plant water-use efficiency and photosynthesis [30,31]. It is particularly important to understand the molecular mechanism underlying the resistance of J. curcas to drought and salinity stress. To date, six versions of whole-genome sequencing data of J. curcas have been reported [[32], [33], [34], [35], [36], [37]], which have served as excellent resources for genome-wide insight into J. curcas. Several J. curcas TFs i.e., WRKYs [38], MYBs [39], and NACs [40] involved in resistance to abiotic stress have been reported. Wang et al. [41] identified bZIP TFs in the third version (Chinese version completed by Wu's team) of genomic data of J. curcas [34] and analyzed the expression patterns of these TFs in J. curcas under low-temperature stress. However, the expression patterns of bZIP TFs in J. curcas under drought and salinity stress remain enigmatic.
In this study, bZIP genes of J. curcas were identified on the basis of whole-genome sequencing. The physicochemical properties of the proteins were predicted, followed by systematic analysis of the evolutionary relationships, genetic structure, cis-acting elements and codon usage bias of the JcbZIP genes, which were analyzed systematically via different bioinformatic tools. Furthermore, the expression patterns of JcbZIP genes in three different tissues (leaf, root and seed) [42], seven different stages of seed development (14 days after pollination (DAP), 19 DAP, 25 DAP, 29 DAP, 35 DAP, 41 DAP and 45 DAP) [43] and under drought [44] and salinity stress conditions [45] were also analyzed. Candidate resistance-related genes were selected on the basis of published transcriptomic data and quantitative real-time PCR (qRT-PCR) results in this study. The results of systematic analysis of the structure, evolution and general biological characteristics of the JcbZIP genes obtained in this study are valuable as a reference for other plant studies. Importantly, these results shed light on the role of JcbZIP TFs in responses to drought and salinity stress. The identification of several pivotal candidate resistance-related genes lays a crucial foundation for the future verification of gene function in transgenic plants.
Section snippets
Collection of sequencing data
The J. curcas data used in this study were derived from the second version of the J. curcas genome-wide sequence database (http://www.kazusa.or.jp/jatropha/; JAT_r4.5; Japanese version, which was completed by Sato's team) [33]. The protein sequences of bZIPs from eight plant species (A. thaliana, O. sativa, P. trichocarpa, S. bicolor, Z. mays, V. vinifera, R. communis and Chaenomeles sinensis) were downloaded from the Plant Transcription Factor Database (http://plntfdb.bio.unipotsdam.de/; v3.0)
Identification of JcbZIP TFs in J. curcas
Following a database search and sequence alignment of known bZIP proteins from eight plant species, we identified 61 candidate TFs containing the bZIP domain. Additionally, a total of 50 nonredundant JcbZIP TFs were also identified by the online SMART toolkit. Subsequently, the candidate JcbZIP genes were identified and named JcbZIPX, where X represents integers i.e., 1 to 50 in ascending order depending on the locations of the genes on the corresponding chromosomes (Table 1).
Characteristics of JcbZIP TFs
The
Discussion
In this work, a total of 50 bZIP genes were identified in J. curcas. 51 bZIP genes were identified by Wang et al. [41] in the third version of the genome (Chinese version, which was completed by Wu's team); 49 bZIP genes were identified in R. communis [22], another euphorbiaceous plant species; and 55 bZIP genes were identified in V. vinifera. The numbers of bZIP genes in these plants were similar to the numbers detected in our study. Phylogenetic analysis categorized the identified bZIP genes
Conclusion
In summary, comprehensive analysis of 50 JcbZIP genes in J. curcas was performed to clarify the overall and molecular characteristics of JcbZIP genes. In addition, expression pattern analysis of JcbZIP genes in different tissues and at various stages of seed development implied that these genes may be involved in the development of J. curcas. Moreover, six JcbZIP genes (JcbZIPs 19, 27, 34, 36, 49 and 50) selected by RNA-seq further verified by qRT-PCR. JcbZIP49 and JcbZIP50 are particularly
Abbreviations
- bZIP
basic leucine zipper
- TF
transcription factor
- aa
amino acid
- ABA
abscisic acid
- HMM
Hidden Markov model
- MW
molecular weight
- PI
isoelectric point
- GSDS
Gene Structure Display Server
- RSCU
relative synonymous codon usage
- RFSC
relative frequency of synonymous codons
- TPM
transcripts per million
- AI
aliphatic index
- ABRE
ABA-responsive element
- PAPD
Priority academic program development
Ethics approval and consent to participate
Not applicable.
Consent for publication
Not applicable.
Availability of data and materials
The data sets supporting the results of this article are included within the article and its additional files.
Funding
This study was supported by the General Project of the Natural Science Foundation of Anhui Province (1708085MC76), the Key Project Support Plan to Excellent Young Talents in Colleges and University at Anhui Province (gxyq2020040), the Open Fund of State Key Laboratory of Tea Plant Biology and Utilization (SKLTOF20200129), the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), the Project of the Provincial Quality Engineering of Colleges and Universities in
CRediT authorship contribution statement
ZJW: Conceptualization, Methodology, Software, Data curation, Validation, Writing - review & editing. JZ: Visualization, Investigation, Writing - original draft, Software. WYY: Visualization, Investigation, Writing - original draft, Software, Writing - review & editing. YW: Software, Data curation, Validation. PPH: Investigation, Writing - original draft, Validation, Writing - review & editing. HMX: Software, Writing - original draft. DDW, QWC: Software, Data curation. JL, CYJ: Software, Data
Declaration of competing interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Acknowledgments
The authors would like to thank the anonymous reviewers for their comments on this manuscript. We are grateful to Prof. Zhong Zhao and Prof. Chengbin Xiang, School of life science, University of Science and Technology of China, and Prof. Enhua Xia, School of Tea and Food Science & Technology, Anhui Agricultural University, for help with revision of our paper.
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2023, International Journal of Biological MacromoleculesCmSCL4 and CmR1MYB1 synergistically enhance the drought tolerance by regulation of ABA signaling in chrysanthemum
2022, Environmental and Experimental BotanyCitation Excerpt :According to the core signaling components model, upon ABA binding, the PYR/PYL/RCAR receptors undergo conformational changes which facilitates the binding affinity to PP2Cs. The inhibition of PP2Cs releases the phosphorylation activities of SNF1-related type 2 protein kinases (SnRK2s) which further phosphorylate various membrane proteins, such as channel proteins and transporters, as well as some bZIP transcription factors which bind to the ABA-responsive elements (ABREs; PyACGTGG/TC) in the promoter regions of downstream target genes (Hauser et al., 2011; Wang et al., 2021). Evidence for function of GRAS type proteins involved in ABA signaling networks has been gradually emerging.
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Zhanjun Wang and Jin Zhu contributed equally to this work.