scholarly journals Genome- and Transcriptome-Wide Characterization of bZIP Gene Family Identifies Potential Members Involved in Abiotic Stress Response and Anthocyanin Biosynthesis in Radish (Raphanus sativus L.)

2019 ◽  
Vol 20 (24) ◽  
pp. 6334 ◽  
Author(s):  
Lianxue Fan ◽  
Liang Xu ◽  
Yan Wang ◽  
Mingjia Tang ◽  
Liwang Liu
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Leucine Zipper ◽  
Anthocyanin Biosynthesis ◽  
Functional Characterization ◽  
Abiotic Stress Response ◽  
Basic Leucine Zipper ◽  
Promoter Sequences ◽  
Encoding Genes

Basic leucine zipper (bZIP) transcription factors play crucial roles in various abiotic stress responses as well as anthocyanin accumulation. Anthocyanins are most abundant in colorful skin radish, which exhibit strong antioxidant activity that offers benefits for human health. Here, a total of 135 bZIP-encoding genes were identified from radish genome. Synteny analysis showed that 104 radish and 63 Arabidopsis bZIP genes were orthologous. Transcriptome analysis revealed that 10 RsbZIP genes exhibited high-expression levels in radish taproot (RPKM>10). Specifically, RsbZIP010 exhibited down-regulated expression under Cd, Cr and Pb stresses, whereas RsbZIP031 and RsbZIP059 showed significant down-regulation under heat and salt stresses, respectively. RT-qPCR analysis indicated that RsbZIP011 and RsbZIP102 were significantly up-regulated in the tissues of radish with high anthocyanin contents. Furthermore, the promoter sequences of 39 anthocyanin-related genes were found to contain G-box or ACE-box elements that could be recognized by bZIP family members. Taken together, several RsbZIPs might be served as critical regulators in radish taproot under Cd, Cr, Pb, heat and salt stresses. RsbZIP011 and RsbZIP102 were the potential participants in anthocyanin biosynthesis pathway of radish. These results facilitate further investigation on functional characterization of bZIP genes in response to abiotic stress and anthocyanin biosynthesis in radish.

scholarly journals Genome-Wide Analysis, Characterization, and Expression Profile of the Basic Leucine Zipper Transcription Factor Family in Pineapple

2020 ◽  
Vol 2020 ◽  
pp. 1-14 ◽  
Author(s):  
Yanhui Liu ◽  
Mengnan Chai ◽  
Man Zhang ◽  
Qing He ◽  
Zhenxia Su ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Leucine Zipper ◽  
Developmental Stages ◽  
Functional Characterization ◽  
Sequencing Data ◽  
Basic Leucine Zipper ◽  
Expression Levels ◽  
Duplication Events

This study identified 57 basic leucine zipper (bZIP) genes from the pineapple genome, and the analysis of these bZIP genes was focused on the evolution and divergence after multiple duplication events in relation to the pineapple genome fusion. According to bioinformatics analysis of a phylogenetic tree, the bZIP gene family was divided into 11 subgroups in pineapple, Arabidopsis, and rice; gene structure and conserved motif analyses showed that bZIP genes within the same subgroup shared similar intron-exon organizations and motif composition. Further synteny analysis showed 17 segmental duplication events with 27 bZIP genes. The study also analyzed the pineapple gene expression of bZIP genes in different tissues, organs, and developmental stages, as well as in abiotic stress responses. The RNA-sequencing data showed that AcobZIP57 was upregulated in all tissues, including vegetative and reproductive tissues. AcobZIP28 and AcobZIP43 together with the other 25 bZIP genes did not show high expression levels in any tissue. Six bZIP genes were exposed to abiotic stress, and the relative expression levels were detected by quantitative real-time PCR. A significant response was observed for AcobZIP24 against all kinds of abiotic stresses at 24 and 48 h in pineapple root tissues. Our study provides a perspective for the evolutionary history and general biological involvement of the bZIP gene family of pineapple, which laid the foundation for future functional characterization of the bZIP genes in pineapple.

scholarly journals Genome-Wide Identification and Expression Analysis of the bZIP Transcription Factors in the Mycoparasite Coniothyrium minitans

2020 ◽  
Vol 8 (7) ◽  
pp. 1045
Author(s):  
Yuping Xu ◽  
Yongchun Wang ◽  
Huizhang Zhao ◽  
Mingde Wu ◽  
Jing Zhang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Gene Family ◽  
Expression Analysis ◽  
Stress Responses ◽  
Leucine Zipper ◽  
Coniothyrium Minitans ◽  
Basic Leucine Zipper ◽  
Bzip Domain ◽  
Conidial Development

The basic leucine zipper (bZIP) proteins family is one of the largest and most diverse transcription factors, widely distributed in eukaryotes. However, no information is available regarding the bZIP gene family in Coniothyrium minitans, an important biocontrol agent of the plant pathogen Sclerotinia sclerotiorum. In this study, we identified 34 bZIP genes from the C. minitans genome, which were classified into 8 groups based on their phylogenetic relationships. Intron analysis showed that 28 CmbZIP genes harbored a variable number of introns, and 15 of them shared a feature that intron inserted into the bZIP domain. The intron position in bZIP domain was highly conserved, which was related to recognize the arginine (R) and could be treated as a genomic imprinting. Expression analysis of the CmbZIP genes in response to abiotic stresses indicated that they might play distinct roles in abiotic stress responses. Results showed that 22 CmbZIP genes were upregulated during the later stage of conidial development. Furthermore, transcriptome analysis indicated that CmbZIP genes are involved in different stages of mycoparasitism. Among deletion mutants of four CmbZIPs (CmbZIP07, -09, -13, and -16), only ΔCmbZIP16 mutants significantly reduced its tolerance to the oxidative stress. The other mutants exhibited no significant effects on colony morphology, mycelial growth, conidiation, and mycoparasitism. Taken together, our results suggested that CmbZIP genes play important roles in the abiotic stress responses, conidial development, and mycoparasitism. These results provide comprehensive information of the CmbZIP gene family and lay the foundation for further research on the bZIP gene family regarding their biological functions and evolutionary history.

scholarly journals Genome-wide characterization of NtHD-ZIP IV: different roles in abiotic stress response and glandular Trichome induction

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Hongying Zhang ◽  
Xudong Ma ◽  
Wenjiao Li ◽  
Dexin Niu ◽  
Zhaojun Wang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Stress Responses ◽  
Leucine Zipper ◽  
Regulatory Gene ◽  
Glandular Trichomes ◽  
Glandular Trichome ◽  
Tissue Expression ◽  
Abiotic Stress Response ◽  
Epidermal Development

Abstract Background The plant-specific homeodomain-leucine zipper class IV (HD-ZIP IV) gene family has been involved in the regulation of epidermal development. Results Fifteen genes coding for HD-ZIP IV proteins were identified (NtHD-ZIP-IV-1 to NtHD-ZIP-IV-15) based on the genome of N. tabacum. Four major domains (HD, ZIP, SAD and START) were present in these proteins. Tissue expression pattern analysis indicated that NtHD-ZIP-IV-1, − 2, − 3, − 10, and − 12 may be associated with trichome development; NtHD-ZIP-IV-8 was expressed only in cotyledons; NtHD-ZIP-IV-9 only in the leaf and stem epidermis; NtHD-ZIP-IV-11 only in leaves; and NtHD-ZIP-IV-15 only in the root and stem epidermis. We found that jasmonates may induce the generation of glandular trichomes, and that NtHD-ZIP-IV-1, − 2, − 5, and − 7 were response to MeJA treatment. Dynamic expression under abiotic stress and after application of phytohormones indicated that most NtHD-ZIP IV genes were induced by heat, cold, salt and drought. Furthermore, most of these genes were induced by gibberellic acid, 6-benzylaminopurine, and salicylic acid, but were inhibited by abscisic acid. NtHD-ZIP IV genes were sensitive to heat, but insensitive to osmotic stress. Conclusion NtHD-ZIP IV genes are implicated in a complex regulatory gene network controlling epidermal development and abiotic stress responses. The present study provides evidence to elucidate the gene functions of NtHD-ZIP IVs during epidermal development and stress response.

scholarly journals A Rice Immunophilin Homolog, OsFKBP12, Is a Negative Regulator of Both Biotic and Abiotic Stress Responses

2020 ◽  
Vol 21 (22) ◽  
pp. 8791
Author(s):  
Ming-Yan Cheung ◽  
Wan-Kin Auyeung ◽  
Kwan-Pok Li ◽  
Hon-Ming Lam
Keyword(s):  
Abiotic Stress ◽  
Pseudomonas Syringae ◽  
Stress Responses ◽  
Biotic Stress ◽  
Higher Plants ◽  
Functional Characterization ◽  
Negative Regulator ◽  
Abiotic Stress Response ◽  
Biotic And Abiotic Stress ◽  
Higher Plant

A class of proteins that were discovered to bind the immunosuppressant drug FK506, called FK506-binding proteins (FKBPs), are members of a sub-family of immunophilins. Although they were first identified in human, FKBPs exist in all three domains of life. In this report, a rice FKBP12 homolog was first identified as a biotic stress-related gene through suppression subtractive hybridization screening. By ectopically expressing OsFKBP12 in the heterologous model plant system, Arabidopsis thaliana, for functional characterization, OsFKBP12 was found to increase susceptibility of the plant to the pathogen, Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). This negative regulatory role of FKBP12 in biotic stress responses was also demonstrated in the AtFKBP12-knockout mutant, which exhibited higher resistance towards Pst DC3000. Furthermore, this higher-plant FKBP12 homolog was also shown to be a negative regulator of salt tolerance. Using yeast two-hybrid tests, an ancient unconventional G-protein, OsYchF1, was identified as an interacting partner of OsFKBP12. OsYchF1 was previously reported as a negative regulator of both biotic and abiotic stresses. Therefore, OsFKBP12 probably also plays negative regulatory roles at the convergence of biotic and abiotic stress response pathways in higher plants.

scholarly journals Genome-wide identification, characterisation, and evolution of ABF/AREB subfamily in nine Rosaceae species and expression analysis in mei (Prunus mume)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10785
Author(s):  
Xue Yong ◽  
Tangchun Zheng ◽  
Xiaokang Zhuo ◽  
Sagheer Ahmad ◽  
Lulu Li ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Stress Responses ◽  
Leucine Zipper ◽  
Ornamental Plants ◽  
Evolutionary Relationship ◽  
Bzip Transcription Factor ◽  
Abiotic Stress Response ◽  
Flower Bud ◽  
Rosaceae Species

Rosaceae is an important family containing some of the highly evolved fruit and ornamental plants. Abiotic stress responses play key roles in the seasonal growth and development of plants. However, the molecular basis of stress responses remains largely unknown in Rosaceae. Abscisic acid (ABA) is a stress hormone involving abiotic stress response pathways. The ABRE-binding factor/ABA-responsive element-binding protein (ABF/AREB) is a subfamily of the basic domain/leucine zipper (bZIP) transcription factor family. It plays an important role in the ABA-mediated signaling pathway. Here, we analyzed the ABF/AREB subfamily genes in nine Rosaceae species. A total of 64 ABF/AREB genes were identified, including 18, 28, and 18 genes in the Rosoideae, Amygdaloideae, and Maloideae traditional subfamilies, respectively. The evolutionary relationship of the ABF/AREB subfamily genes was studied through the phylogenetic analysis, the gene structure and conserved motif composition, Ka/Ks values, and interspecies colinearity. These gene sets were clustered into four groups. In the Prunus ABF/AREB (PmABF) promoters, several cis-elements related to light, hormone, and abiotic stress response were predicted. PmABFs expressed in five different tissues, except PmABF5, which expressed only in buds. In the dormancy stages, PmABF1, 2, 5 and 7 showed differential expression. The expression of PmABF3, 4 and 6 was positively correlated with the ABA concentration. Except for PmABF5, all the PmABFs were sensitive to ABA. Several ABRE elements were contained in the promoters of PmABF1, 3, 6, 7. Based on the findings of our study, we speculate that PmABFs may play a role in flower bud dormancy in P. mume.

scholarly journals Functional Characterization of DEAD-Box RNA Helicases in Arabidopsis thaliana under Abiotic Stress Conditions

2008 ◽  
Vol 49 (10) ◽  
pp. 1563-1571 ◽  
Author(s):  
Jin Sun Kim ◽  
Kyung Ae Kim ◽  
Tae Rin Oh ◽  
Chul Min Park ◽  
Hunseung Kang
Keyword(s):  
Arabidopsis Thaliana ◽  
Abiotic Stress ◽  
Functional Characterization ◽  
Stress Conditions ◽  
Rna Helicases ◽  
Dead Box

Systematic discovery and characterization of stress-related microRNA genes in Oryza sativa

Biologia ◽  
2015 ◽  
Vol 70 (1) ◽  
Author(s):  
Kai Bin Xie ◽  
Xue Zhou ◽  
Tian Hai Zhang ◽  
Bao Long Zhang ◽  
Li Ming Chen ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Systematic Investigation ◽  
Chemical Toxicity ◽  
Promoter Regions ◽  
Crop Species ◽  
Translation Inhibition ◽  
Microrna Genes ◽  
Insight Into

AbstractAbiotic stresses including drought, salinity, extreme temperatures, chemical toxicity and oxidative are the natural status of the environment to exert serious threats to agriculture. Abiotic stress-related microRNAs (ASmiRNAs) are a group of microRNAs (miRNAs) regulating stress responses in plants. However, the systematic investigation of ASmiRNAs is limited in Rice (O. sativa), a typical abiotic stress-resistant crop species. In the present work, we systematically investigated ASmiRNAs in silico. First, we identified 177 putative ASmiRNAs in O.sativa. Second, we found most ASmiRNAs were driven by TATA-promoter and most stress-related miRNA promoter regions contained the stress-related elements. Third, we found many ASmiRNAs families were species/family specific and a set of miRNAs might derive from genomic repeat-sequences in O. sativa. Finally, we found the ASmiRNAs in O. sativa target 289 genes with 1050 predicted target sites in which 98% sites have cleavage activity and 2% sites have translation inhibition activity. In conclusion, our findings provide an insight into both the function and evolution of ASmiRNAs and improve our understanding on the mechanism of abiotic stress resistance in O. sativa.

Genome-wide systematic characterization and its regulatory expression reprogramming process of the bZIP transcription factors during trauma response in Camellia sinensis

2018 ◽  
Vol 48 (11) ◽  
pp. 1279-1291
Author(s):  
Yajie Xue ◽  
Zaibao Zhang ◽  
Lei Wang ◽  
Yajun Yu ◽  
Jinbin Xiao ◽  
...  
Keyword(s):  
Phylogenetic Relationship ◽  
Camellia Sinensis ◽  
Leucine Zipper ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Gene Expression Profiles ◽  
Bzip Transcription Factor ◽  
Motif Analysis ◽  
Basic Leucine Zipper ◽  
Tea Tree

Basic leucine zipper (bZIP) transcription factor (TF) genes regulate numerous biological processes, as well as biotic and abiotic responses. Although the genome of the tea tree (Camellia sinensis (L.) Kuntze) has been released, knowledge regarding the bZIP TF family in C. sinensis, e.g., phylogenetic relationship and transcriptional gene expression profiles, remains limited. In this study, we characterized 77 bZIP genes in C. sinensis based on transcriptomic and genomic data and divided them into 11 groups according to their phylogenetic relationship with those in Arabidopsis, which allowed us to identify 14 pairs of orthologous proteins shared by Arabidopsis and C. sinensis and 19 pairs of paralogous proteins in C. sinensis. Conserved motif analysis of CsbZIP proteins showed high group specificity. Our classification was supported by the predicted specificities based on DNA-binding domains, as well as the dimerization property based on characteristic features in the basic and hinge regions and the leucine zipper. Specifically, they indicated that some highly conserved amino acid residues exist across each major group in the tree of land plant life. Expression profiling analyses indicate that the CsbZIP genes are likely involved in response to trauma, and a model was established to display the unique expression of each group during different time intervals after wounding. This work provides useful clues for further functional characterization of the CsbZIP TFs.

scholarly journals The Construction of Plant Expression Vector harbouring Carica Papaya L. WRKY Gene in Escherichia coli

2020 ◽  
Vol 28 (S2) ◽  
Author(s):  
Fauziah Abu Bakar ◽  
Pavitra Paramalingam ◽  
Kamariah Hasan
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Expression Vector ◽  
Carica Papaya ◽  
Sequencing Analysis ◽  
Wrky Gene ◽  
Limited Information ◽  
Abiotic Stress Response ◽  
Plant Expression ◽  
Plant Expression Vector

Carica papaya is a well-liked and economically important fruit with outstanding nutritional and medicinal values. Its susceptibility to abiotic stress which affects the growth and harvest, causes significant yield loss to farmers. In recent years, significant progress has been made to understand the genes that play critical roles in abiotic stress response, especially some transcription factor (TF) encoding genes. Among all TFs, WRKY TF gene family is one of the best-studied TFs involved in various stress responses. To date, only limited information on functionally characterised WRKY TFs is available for C. papaya. The aim of this study was to produce a recombinant construct harbouring WRKY gene in pGEM®-T Easy cloning vector. The presence of a DNA band of the expected size of 465 bp on agarose gel electrophoresis indicated that WRKY gene was successfully amplified from all treated samples. DNA sequencing analysis revealed that the amplified sequence isolated from the treated samples were closely related to Carica papaya species with 97% similarity. Following transformation, 4 out of 5 colonies that were randomly selected showed the WRKY gene had been successfully inserted into pGEM®-T Easy vector and transformed into E. coli. In future, the WRKY gene from pGEMT-WRKY recombinant construct will be cloned into the plant expression vector pCAMBIA 1304 prior to transformation in the plant. The success of demonstrating the WRKY gene towards the response in abiotic stress will enable us to produce stress tolerant transgenic crops under unfavourable conditions via genetic engineering for sustained growth.

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