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Article

Genome-Wide Analysis of ZAT Gene Family in Osmanthus fragrans and the Function Exploration of OfZAT35 in Cold Stress

by
Huifen Ding
1,2,
Zhandong Yang
1,2,
Zhouying Zai
1,2,
Keyi Feng
1,2,
Lianggui Wang
1,2,
Yuanzheng Yue
1,2 and
Xiulian Yang
1,2,*
1
Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
2
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
*
Author to whom correspondence should be addressed.
Plants 2023, 12(12), 2346; https://0-doi-org.brum.beds.ac.uk/10.3390/plants12122346
Submission received: 31 March 2023 / Revised: 4 June 2023 / Accepted: 12 June 2023 / Published: 16 June 2023
(This article belongs to the Section Plant Response to Abiotic Stress and Climate Change)
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Abstract

:
Osmanthus fragrans is a popular ornamental and odorant plant with high commercial value, but its cultivation and exploitation are limited by low temperature. The ZAT (zinc finger of Arabidopsis thaliana) genes as a subclass of the C2H2-type zinc finger proteins (C2H2-ZFP) family play essential roles in various abiotic stresses. However, their roles in cold stress response in O. fragrans remain unclear. This study identified 38 OfZATs, which could be divided into 5 subgroups based on the phylogenetic tree, with OfZATs in the same subgroup harboring similar gene structures and motif patterns. In addition, 49 segmental and 5 tandem duplication events were detected among OfZAT genes, while some OfZAT genes exhibited specific expression patterns in different tissues. Furthermore, two OfZATs were induced in salt stress and eight OfZATs responded to cold stress. Interestingly, OfZAT35 showed a continuously increasing expression trend under cold stress, while its protein showed nucleus localization with no transcriptional activation activity. Transiently transformed tobacco overexpressing OfZAT35 exhibited a significantly higher relative electrolyte leakage (REL) level and increased activities of superoxide dismutase (SOD), peroxidase (POD), and Ascorbate peroxidase (APX), while there was significantly decreased activity of catalase (CAT). Moreover, CAT, DREB3, and LEA5, which are associated with cold stress, were dramatically decreased after cold treatment in transiently transformed tobacco, suggesting that overexpression of OfZAT35 negatively regulated cold stress. This study provides a basis for exploring the roles of ZAT genes and contributes to uncovering the mechanism of ZAT-mediated cold stress response in O. fragrans.

1. Introduction

Osmanthus fragrans is an ever-green, small ornamental tree or shrub, which is famous for its fragrant flowers and high commercial value. The O. fragrans flowers can be processed into food additives in pastries and drinks, such as tea, while its flower extracts are known to produce one of the best natural fragrant essences [1]. Due to its commercial benefits, the color and flower fragrance have become trending research topics in O. fragrans [2,3,4]. Osmanthus mostly grows in the warm temperature region of Asia [5]. The cultivation and commercial exploitation of the species O. fragrans is however limited by low temperature [6]. Therefore, low temperature is a key factor in osmanthus breeding. Several molecular studies on the O. fragrans response to cold stress have recently been reported. The genes of the bHLH transcription factor (TF) in O. fragrans induced by cold stress were screened through quantitative real-time PCR (qRT-PCR), while the functions of the NAC TF family in response to cold stress in O. fragrans were also screened using qRT-PCR [7,8]. The overexpression of an O. fragrans heat shock factor OfHSF11 in tobacco (Nicotiana benthamiana) under cold stress could negatively impact transgenic plant responses to cold treatment [9]. However, the molecular mechanism of sweet osmanthus response to low temperature stress is still unclear.
TFs are genes that regulate signal transduction and gene transcription, and their regulatory activities are associated with plant abiotic stress responses, such as cold stress [10]. The C2H2 zinc finger proteins (ZFPs) TF family was divided into many subfamilies, among which the C1 family is one of the largest subfamilies [11]. The members of the C1 family have different numbers of dispersed zinc fingers and were classed into five subclasses, including C1-1i, C1-2i, C1-3i, C1-4i, and C1-5i [11,12,13]. ZAT genes code the proteins which contain two dispersed zinc fingers and constitute the subclass C1-2i of the C2H2-ZFP TF family. [11,12]. Furthermore, most members of the ZAT family also have a highly conserved QALGGH motif and an EAR motif at the C-terminus [12]. To date, the systematic identification of members in the ZAT family has been performed in numerous plants, such as Petunia hybrida, A. thaliana, Triticum aestivum, Gossypium hirsutum, Fragaria × ananassa, and Populus trichocarpa [11,13,14,15,16,17]. However, despite their potential crucial roles in cold stress response, members of the ZAT gene family have yet to be characterized in O. fragrans.
The roles of ZAT genes have been reported in responding to cold stress and other abiotic stresses, with some members playing crucial regulatory roles in cold stress pathways [18]. Transcriptomic analyses have shown that the ZAT genes are significantly differentially expressed under cold stress in herbaceous plants, such as Vicia sativa, Nicotiana tabacum, and Brassica napus, as well as woody plants, such as Taxillus chinensis, Citrus reticulata ‘Chongyi’, and Jatropha curcas [19,20,21,22,23,24]. Studies on the ZAT gene family responses to cold and other stresses have extensively been reported in Arabidopsis. For example, the Arabidopsis ZAT6, ZAT7, ZAT10, and AZF2 genes have been shown to be responsive to cold, dehydration, and high-salt stress, with some enhancing cold stress tolerance in the plant [25,26,27]. The cold responsive regulatory mechanism of AtZATs has also been reported. The cold stress-responsive RD29A gene is a target of CBF, and its transcription is repressed by AtZAT10, leading to enhanced cold tolerance [28]. In addition, AtZAT12 could affect cold tolerance in Arabidopsis by directly repressing CBF and also through the regulation of non-CBF signaling pathway genes during cold stress [29,30,31].
In this study, the published genome-wide sequence and transcriptome of O. fragrans were screened to characterize the ZAT gene family and to explore their expression profiles in various organs or tissues and under cold and salt stresses [4,9,32]. As a result, 38 ZAT genes were identified. Phylogenetic classification, duplication events, subcellular localization prediction, gene structure analysis, and expression patterns in various organs or tissues and under cold and salt stresses were performed. Based on gene expression patterns, a candidate OfZAT35 gene was selected and transiently overexpressed in tobacco to investigate its likely function in cold stress. Our works not only provide a foundation for the functional evaluation of ZAT genes, but also contribute to uncovering the molecular regulatory mechanism of cold stress response in O. fragrans.

2. Results

2.1. Identification, Distribution, Duplication, and Physicochemical Characteristics of OfZATs

Thirty-eight candidate ZAT genes identified using HMMER 3.0 and tagged as OfZAT1–38 based on their chromosomal locations were identified in the O. fragrans genome (Figure 1). Except for chromosomes (Chr) 1, 2, 4, 8, 9, 18, 19, and 20, ZAT genes were unevenly scattered across 15 O. fragrans chromosomes, with the highest density of 10 genes being observed in Chr 11, while other chromosomes contained 1–5 ZAT gene members.
The analysis of ZAT gene duplication events using the MCScanX program identified 49 segmental and 5 tandem duplication events in the O. fragrans genome (Figure S1). The 5 tandem duplication events occurred in 13 genes, including OfZAT3/4, OfZAT10/11, OfZAT12/13, OfZAT16/17, and OfZAT18/19/20/21/22, which were detected in Chr 5, Chr 10, and Chr 11. Additionally, 49 segmental duplication events were observed in 27 genes, which demonstrated that the ZAT gene family predominantly originated from segmental and tandem duplication events.
The physicochemical evaluation of OfZATs revealed that the predicted protein molecular weight (MW) ranged from 19.50 to 55.83 kDa in OfZAT13 and OfZAT37, respectively, while the isoelectric point (pI) varied from 6.11 in OfZAT17 to 9.73 in OfZAT4. Moreover, the prediction of subcellular localization exhibited that all predicted OfZATs are located in the nucleus (Table S1).

2.2. Phylogenetic Analysis of ZAT Genes

The 38 predicted OfZATs along with 20, 20, and 11 homologous genes retrieved from Arabidopsis (A. thaliana), rice (Oryza sativa), and black cottonwood (P. trichocarpa), respectively, were used for phylogenetic tree construction with the neighbor-joining (NJ) method to explore their evolutionary relationships. According to the types of motifs (Figure S2), the 89 genes could be clustered into 5 subgroups, including ZAT-A, ZAT-B, ZAT-C, ZAT-D, and ZAT-E (Figure 2). The sequences of motifs are displayed in Table S2. Notably, ZAT-A was the largest subgroup containing 25 genes, while ZAT-C was the smallest subgroup with 11 members.

2.3. Structure and Motif Composition of OfZATs

To further analyze the evolutionary relationships among OfZATs, their structural and motif composition were analyzed (Figure 3). A varied number of exon–intron distributions were observed among OfZAT genes. Interestingly, introns were absent in most OfZATs, with only five genes (OfZAT1/3/6/29/30) having one intron in their sequences. Motif identification using the MEME tool revealed 15 conserved OfZATs motifs, with OfZAT proteins in the same subgroup harboring similar motifs in both position and type. For example, members of the ZAT-B subgroup all contained Motifs 3, 2, 1, 10, 4, and 9 with similar permutations, while most members of the ZAT-A subgroup contained Motifs 5, 3, 2, 1, 4, and 9 with a similar permutation. Notably, Motif 5 was only absent in OfZAT1. In addition, most OfZATs contained Motif 1, Motif 2, and Motif 3. Motif 1 contains the conserved sequence CX2CX3FX2GQALGGHX3H, which was reported as first zinc finger domain, and the conserved sequence CX2CX3FX3QALGGHX3H in Motif 2 (Table S3) was reported as the second zinc finger domain (X represents arbitrary amino acid, and the number represents the quantity of amino acid) [18]. Motif 3 contains the conserved sequence AX2LX2L (Table S3), while the conserved sequence has not been reported. The sequences of the 15 motifs are displayed in Table S3.

2.4. Cis-Elements Analysis in OfZATs

The promoter screening of OfZATs was performed to facilitate the prediction of their potential biological functions. After excluding the universal, incomplete, and unannotated cis-elements, a total of 32 cis-elements, which were associated with four categories, including hormones, stress, development, and light responses, were identified (Figure S3). The hormone category contained 11 cis-elements, which were associated with the regulation of abscisic acid (ABA), methyl-jasmonate (MeJA), gibberellin (GA), Auxin, and salicylic acid (SA). Of the 38 predicted OfZATs, 32 (84.21%) contained 109 ABRE cis-elements, which are associated with the ABA response pathway, while 30 OfZATs (78.95%) contained 76 CGTCA and 76 TGACG-motifs, which are related to MeJA regulation. The development and light categories contained 8 cis-elements, and 31 genes (81.58%) harbored 109 G-boxes that are associated with light response. The stress group contained six cis-elements related to anaerobic induction, drought, wound, and low temperature stress. These results suggested that most members of the ZAT family in O. fragrans might potentially be involved in the ABA, MeJA, and light response processes, which provide a reference for further investigation.

2.5. Expression Pattern of OfZAT Genes in Different O. fragrans Tissues

The fragments per kilobase million (FPKM) values of OfZATs in four tissues, including the root, stem, leaves, and flowers, were obtained from previously reported transcriptome data (Table S4) which have been published in NCBI (SRP143423) [4]. The heat map was generated using TBtools according to the FPKM values from the transcriptome (Figure 4). Generally, FPKM values between 0 and 1 were considered as low expression levels [33]. Here, nine genes (OfZAT2/6/18/22/23/24/28/30/37) with low expression profiles were detected, while five genes (OfZAT16/17/19/20/21) were not expressed in all tissues (FPKM = 0) (Figure 4). In the root, there were seven OfZATs (OfZAT8/15/25/29/32/35/36) expressed highly (FPKM > 10), among which the expression level of OfZAT35 was the highest (FPKM = 200.82). In the stem, most OfZATs were not expressed or poorly expressed, and only OfZAT8 was expressed. In the leaf (both young and mature), only two OfZATs (OfZAT8/36) were expressed highly. In the flower, there were 10 OfZATs (OfZAT5/7/8/14/15/25/31/35/36/38) expressed highly. OfZAT7 and OfZAT38 exhibited the highest expression level in the full blooming stage among three flowering stages. However, the expression levels of eight OfZATs (OfZAT5/8/14/15/25/31/35/36) were highest at the flower fading stage during three flowering stages. Numerous genes have been shown to exhibit unique expression profiles in specific tissues, and the observed preferential tissue specific expression of OfZATs suggested their broad participation in plant growth and development.

2.6. Expression Patterns of OfZATs under Salt Stress

For salt treatment, the seedlings were planted in 1/2 Hoagland’s nutrient solution with 250 mM NaCl solution and set at four time points (S0, S6, S24, and S72 h) to collect samples for transcriptome sequencing. In addition, the seedlings of the control group for salt stress were soaked in 1/2 Hoagland nutrient solution and also set at four time points (S0, CK6, CK24, and CK72 h) to collect samples for transcriptome sequencing. The values of FPKM were extracted from unpublished transcriptome data (Table S5) and submitted to TBtools to generate the heat map (Figure S4). As a result, four genes (OfZAT8/25/35/36) showed higher expression levels (FPKM > 10), while the remaining exhibited low (FPKM < 1) or no expression (FPKM = 0) under salt stress (Figure S4). The expression trends of OfZAT25 and OfZAT35 were decreased overall during salt treatment. However, the expression trends of OfZAT25 and OfZAT35 were also decreased in the control. In contrast, the levels of OfZAT8 and OfZAT36 exhibited an increasing trend under salt treatment, but with a decreasing pattern in the control treatment, which suggested that OfZAT8 and OfZAT36 play pivotal roles in salt stress response (Figure 5).

2.7. Expression Patterns of OfZATs under Cold Stress

During the 4 °C cold treatment, the samples were collected at seven timepoints (C0, C3, C12, C24, C72, and C120 h during cold treatment, and after recovery Cr72 h) for transcriptome sequencing. The values of FPKM were extracted from unpublished transcriptome data (Table S6) and submitted to TBtools to generate the heat map. Strong expression profiles (FPKM > 10) were only observed in eight OfZAT genes under cold treatment. In contrast, 29 genes (76.32%) were unresponsive to cold stress (FPKM ≤ 1), of which 10 genes (26.32%) were not expressed (FPKM = 0) in all stages (Figure S5). Under cold treatment, OfZAT7 and OfZAT38 were only upregulated at 0–3 h, and then downregulated in later stages. Five genes, including OfZAT8/25/26/29/32, were continuously upregulated 0–24 h before their overall expression levels decreased in the later periods. Both OfZAT35 and OfZAT36 were dramatically upregulated 0–72 or 0–120 h during cold treatment, and then decreased to a pre-treatment (0 h) level (Figure 6). Subsequently, qRT-PCR analysis was performed in five genes (OfZAT25/26/29/32/35). (Figure 7). As a result, consistent expression patterns were observed between the selected genes and those of transcriptome data in all stages, which demonstrated the reliability of RNA-seq data. Based on its unique expression level dynamics at different intervals after stress exposure, the OfZAT35 gene was selected as a candidate for further investigation.

2.8. Subcellular Localization and Transcriptional Activation Activity

The coding sequence of OfZAT35 was amplified and fused into 35S::GFP plasmids. The empty 35S::GFP vector and 35S::GFP-OfZAT35 vector were transfected into leaves of 30 d tobacco (N. benthamiana), respectively. The fluorescent signals from the leaves revealed that the OfZAT35 protein was only located in the nucleus, indicating its involvement in nucleus functions (Figure 8a). Moreover, pGBKT7-OfZAT35 was also constructed using homologous recombination and then introduced to the AH109 yeast strain for a transcriptional activation activity assay. The yeast strains of the negative control (empty vector pGBKT7) and recombinant plasmids pGBKT7-OfZAT35 grew in a different element deficient culture medium of SD/-Trp, SD/-Trp-Ade, and SD/-Trp-Ade + X-α-gal medium. OfZAT35 and the negative control grew well in SD/-Trp medium, but not in other media, which indicated the absence of its transcriptional activation activity (Figure 8b).

2.9. Analysis of Physiological Parameters

The fused Super1300-OfZAT35 plasmids and empty Super1300 vector (EV) were transfected into leaves of 30 d tobacco (N. benthamiana) by an Agrobacterium-mediated transient expression method. Then, the transiently transformed tobaccos of OfZAT35 and EV were treated for 6 hours under 4 °C. The OfZAT35 was overexpressed according to the result of semi-quantitative RT PCR (sqRT-PCR) (Figure 9a). After 6 h of cold treatment at 4 °C, the relative electrolyte leakage (REL) of transiently transformed tobacco was significantly increased compared to that of the empty vector (EV) (Figure 9b), and the REL level is widely used as an indicator of cell membrane damage [34,35]. Thus, we speculated that the transiently transformed tobacco suffered more intense stress than the EV after 6 h cold treatment at 4 °C.
The activities of superoxide dismutase (SOD), peroxidase (POD), and Ascorbate peroxidase (APX) were significantly increased in the transiently transformed tobacco compared to the EV under cold stress (Figure 9d). However, the activity of catalase (CAT) was significantly reduced (Figure 9d). Notably, the expression levels of NbAPX and NbCAT were consistent with the activities of APX and CAT, respectively (Figure 9c). To analyze the response mechanism of transiently transformed tobacco to cold stress, the expression profiles of cold-related genes were determined using qPCR. The results showed that the levels of NbDREB3 and NbLEA5 were significantly decreased (Figure 9c). Overall, transiently transformed tobacco overexpressing OfZAT35 displayed more cold stress effects than EV plants.

3. Discussion

In this study, 38 members of the ZAT family in O. fragrans were identified, and the number is higher than the number reported in the herbaceous A. thaliana (20) and O. sativa (20) plants or in the woody plant P. trichocarpa (11) [11,14,36]. Synteny analysis detected 49 segmental and 5 tandem duplication events in the OfZAT genes (Figure S1). Large genomic duplication events are known to drive the evolution and expansion of gene families [37,38,39]. For example, the A. thaliana genome has undergone at least 4 major duplication events between 100 and 200 million years ago (MYA), with segmental and tandem duplication contributing to the generation and maintenance of gene families [37,40]. Correspondingly, the O. fragrans genome has experienced 2 duplication events that occurred approximately 14 MYA, which might have contributed to the larger size of the OfZAT gene family [4].
The 38 candidate OfZAT genes were divided into 5 subgroups, and the genes within the same subgroup displayed similar motif types and arrangement, indicating that OfZATs in the same subgroup may have a similar function, and the classification of OfZATs was reliable (Figure 3). Motif 1, Motif 2, and Motif 3 are present in most OfZAT members, and Motif 1, Motif 2, and Motif 3 were also found in most ZAT proteins of A. thaliana, O. sativa, and P. trichocarpa (Figure S2). Similarly, Motif 1, Motif 2, and Motif 3 have been reported in most members of the ZAT protein family in herbaceous plants, such as Fragaria × ananassa [17]. This indicated that the three ZAT motifs might be conserved in different plant species, and their similar clustering in same subgroup demonstrated the reliability of phylogenetic tree clusters. The structural analysis revealed the absence of introns in most OfZAT genes (Figure 3c), which was consistent with the observations made in G. hirsutum and P. trichocarpa [14,16]. Introns are predicted to delay regulatory responses, and genes with fewer introns are rapidly activated during stress [41]. In addition, most OfZATs contained only one exon, indicating their capacity to rapidly respond to environmental stresses. Cis-elements enable the binding of TFs and gene transcription [42]. Most OfZATs contained four types cis-elements associated with hormones, stress, development, and light responses (Figure S3), which suggested their potential functions in correlated reaction pathways.
Normally, the tissue-specific expression of genes implies their potential roles. For example, AtERF102, AtERF103, AtERF104, and AtERF105, which are predominantly expressed in root tissues, are cold stress regulator genes [43]. In this study, the differentially expressed ZATs in O. fragrans tissues might crucially be involved in the plant growth and developmental processes. The genes involved in abiotic stress usually exhibited a differential expression profile in stress. For example, AtZAT10 (STZ) responded to salt stress obviously and improved the resistance for salt stress [44]. OfZAT8 and OfZAT36 were strongly induced in salt stress and have a close phylogenetic relationship with AtZAT10, suggesting that the two genes are crucial for salt stress.
The expression of OfZAT35 was upregulated under long-term cold treatment (Figure 8). Interestingly, AtAZF2, AtZAT10, and AtZAT6, which are cold stress responsive and regulators in Arabidopsis, were phylogenetically closely clustered with the candidate OfZAT35 gene (Figure 1) [18,28]. Taken together, these results strongly suggested that OfZAT35 might also play pivotal roles in cold stress response in O. fragrans. The OfZAT35 protein was shown to be localized in the nucleus, which indicated its in-nucleus activity during cold stress response (Figure 8a). However, OfZAT35 exhibited no transcriptional activation activity (Figure 8b). A similar phenomenon was also discovered in other ZFPs. For example, FaZAT10 exhibited no transcriptional activation activity in strawberry [17]. In Capsicum annuum, the full-length CAZFP1 protein had no transcriptional activation activity [45]. Previous research has revealed that ZFPs regulate gene transcription and expression by interacting with other ZFPs to bind to other DNA sequences [44,46,47]. Thus, the OfZAT35 protein may interact with other proteins to regulate the expression of related genes and reduce cold tolerance. In addition, transiently transformed tobacco has been verified that overexpressed OfZAT35 (Figure 9a) and showed a significantly higher REL level than in EV (p < 0.05) (Figure 9b). The REL is a decisive parameter for predicting the damage to the membrane system [48]. For example, the ectopic expression of MdCDPK1a could improve cold stress tolerance in N. benthamiana by reducing the REL value after cold stress exposure [49]. Similarly, the ectopic expression of RmICE1 from Rosa multiflora enhanced cold stress tolerance in N. benthamiana and reduced the REL value after cold treatment [50]. Thus, the observed higher levels of REL indicated that OfZAT35 overexpression reduced cold stress tolerance in O. fragrans. In addition, the activities of SOD, POD, and APX were all significantly increased, while that of CAT was dramatically decreased (Figure 9d). Correspondingly, the expression levels of NbSOD, NbAPX, and NbCAT were consistent with the activities of SOD, APX, and CAT (Figure 9c). Generally, the activities of antioxidant enzymes are induced when the plant is exposed to abiotic stress and could represent plant responses to adverse conditions [51]. The more significantly increased activities of SOD, POD, and APX in transiently transformed tobacco of OfZAT35 may indicate that the overexpression of OfZAT35 makes antioxidant enzymes more active to respond to cold stress. Furthermore, previous research has revealed that the CAT gene can reduce ROS levels to enhance cold tolerance [52,53]. Consequently, the decreased activity of CAT and expression level of NbCAT suggested that the transiently transformed tobacco of OfZAT35 may accumulate an ROS level and exhibit more sensitivity to cold stress. DREB/CBF and LEA are essential genes that modulate cold stress, and the accumulation of their transcripts is positively correlated with enhanced cold tolerance [54,55,56]. The expression levels of NbDREB3 and NbLEA5 were significantly decreased (Figure 9c) and implied that OfZAT35 is a likely negative regulator of cold stress tolerance in O. fragrans.

4. Materials and Methods

4.1. Plant Materials and Treatments

Two-year-old cuttings of O. fragrans cv. ‘Rixianggui’ originated from Nanjing Forestry University in a previous study. Before application of abiotic treatments, seedlings with good development and consistent growth were selected and transferred to the growth chamber for one week. For cold treatment, the growth chamber temperature was adjusted to 4 °C, while other parameters were maintained [9]. During the cold treatment, we set seven timepoints (0, 3, 12, 24, 72, and 120 h during cold treatment, and after recovery 72 h) to collect the first two leaf pairs from seedlings as samples, and each timepoint set three biological replicates. For salt treatment, with other conditions maintained, the seedlings were planted in 1/2 Hoagland’s nutrient solution with 250 mM NaCl solution, and at four time points (0, 6, 24, and 72 h), we collected the first two leaf pairs from each biological replication as a sample for subsequent analyses. In addition, the seedlings of control group for salt stress were set by soaking in 1/2 Hoagland nutrient solution as previously described [32]. The samples were stored at −80 °C in a freezer.

4.2. Identification, Phylogenesis, Chromosomal Localization, Synteny, and Physicochemical Analysis of OfZATs

All protein-coding OfZAT gene sequences were obtained by genome-wide screening of O. fragrans sequence data [5]. The hidden Markov model (PF13912) was downloaded from the online database (http://pfam.xfam.org/ (accessed on 31 October 2022)) [16]. The HMMER 3.0 software was used to identify candidate OfZAT genes [57]. To examine the accuracy of conserved domains of the candidate OfZAT genes, the online tool CDD search (http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/ (accessed on 1 November 2022)) was used to verify the conserved domains. Moreover, physicochemical properties, such as pI and MW, were evaluated using an online tool (http://web.expasy.org/computepi (accessed on 31 October 2022)) [58]. Prediction of subcellular location was also performed using an online tool (https://wolfpsort.hgc.jp (accessed on 31 October 2022)) [59].
In total, 89 ZAT genes were retrieved from TAIR (https://www.arabidopsis.org/ (accessed on 10 November 2022)) and Phytozome13 (https://phytozome-next.jgi.doe.gov/ (accessed on 10 November 2022)), and their phylogenetic relationships assessed with the NJ method with 1000 bootstrap replications in MEGA 11.0 software [60].
The chromosomal locations of OfZAT genes were analyzed using TBtools based on the O. fragrans genome annotation files. The duplication events in ZAT family were determined using MCScanX (Multiple Collinearity Scan toolkit) program in TBtools, and the results were collected and then visualized using the advanced Circos program [61,62].

4.3. Gene Structure, Conserved Motif Compositions, and Cis-Element Analysis

TBtools was utilized to map the conserved domains of ZAT genes [63]. The motifs were forecasted through MEME tool (http://meme-suite.org/tools/meme (accessed on 7 November 2022)) [64]. A 2 kb genome sequence spanning the promoter regions of OfZAT genes was retrieved and screened for promoters using PlantCARE (https://bioinformatics.psb.ugent.be/webtools/plantcare/html (accessed on 7 November 2022)) [65]. The gene structure, motifs, and cis-elements of ZATs were visualized in TBtools [63].

4.4. Expression Profiles of OfZATs in Tissues under Abiotic Stress

The FPKM values of OfZATs in four tissues, including the root, stem, leaves, and flowers, were obtained from previously reported transcriptome data which have been published in NCBI (SRP143423) [4]. In addition, the expression patterns of OfZATs during cold and salt stress were also analyzed based on the unpublished transcriptome data, and the expression results were visualized with heat maps in TBtools [63].

4.5. RNA Extraction and qRT-PCR

The extraction of total RNA and the synthesis of cDNA from the frozen leaf samples of O. fragrans were performed as in a previous study [9]. Primer 5.0 [66] was utilized to design specific primers for OfZAT25, OfZAT26, OfZAT29, and OfZAT35 (Table S7). OfRNA was used to normalize the data analysis of qRT-PCR [7,67]. The reaction system of qRT-PCR was composed of 0.4 μL primer (forward and reverse primer, respectively), 5 μL SYBR, 0.2 μL ROX, 3 μL ddH2O, and 1 μL cDNA. The reaction condition was set as in a previous study [68].
The protocols of total RNA isolation from transiently transformed tobacco leaves and synthesis of cDNA were performed as in a previous study [9]. A semi-quantitative (sqRT-PCR) analysis was performed to verify the positive overexpression of OfZAT35 in tobacco, and Nbactin was selected as reference gene (Table S7). The mix reaction solution of sqRT-PCR was composed of 1 μL cDNA, 1 μL primer, 10 μL 2 × Rapid taq, and 7 μL ddH2O. The primers of NbSOD, NbCAT, NbP5CS, NbDREB3, and NbLEA5 for qRT-PCR are displayed in Table S8 [9]. Meanwhile, Nbactin was used as a normalizer for the qRT-PCR analysis. The qRT-PCR data were analyzed using the 2−ΔΔCT method, and the results were statistically analyzed in SPSS 20.0 [7].

4.6. Subcellular Localization and Transcriptional Activation Activity of OfZAT35

Specific primers were designed for cloning the full-length CDS sequence of OfZAT35 into the Super1300 vector between Hind III and Kpn I restriction sites to construct the 35S::OfZAT35-GFP fusion vector followed by a positive validation test (Table S9). The 35S::OfZAT35-GFP fusion vector and an EV were introduced into GV3101 (Agrobacterium tumefaciens), respectively, and incubated in Luria–Bertani culture with the following conditions: 28 °C, 200 rpm, 10 h. Then, OfZAT35 and EV were injected into the leaves of 30-day-old tobacco plants, respectively. Transformed tobacco plants were incubated for 2 d in a growth room [9,32]. Finally, the fluorescent signals in the transgenic leaves were detected through an LSM710 microscope (Zeiss, Jena, Germany). Moreover, the whole ORF of OfZAT35 was inserted into GAL4 DNA-binding domain between Smal I and Sal I restriction sites in pGBKT7 plasmid for transcriptional activation activity assay (primers are displayed in Table S8). The empty vector pGBKT7 (negative control) and fused vector pGBKT7-OfZAT35 were introduced into AH109 yeast strain, respectively. Then, the yeast strain of pGBKT7-OfZAT35 and pGBKT7 were respectively incubated in SD/Trp culture with the following conditions: 30 °C and 200 rpm until the value of OD600 reached 0.6. The yeast strains of pGBKT7-OfZAT35 and pGBKT7 in 2 mL SD/Trp culture were collected into 100 μL ddH2O, and then diluted into different dilution multiples (100, 10−1, 10−2, 10−3, and 10−4). The different dilution multiples solution of pGBKT7-OfZAT35 and pGBKT7 was incubated in different nutrient deficient media (SD/-Trp, SD/-Trp-Ade, and SD/-Trp-Ade + X-α-gal medium) under 30 °C.
Transiently transformed tobacco was generated as described for subcellular location. Transiently transformed tobacco was exposed to cold stress treatment at 4 °C in the growth chamber for 6 h. Samples were then collected and frozen by liquid nitrogen. The samples were stored at −80 °C in a freezer for RNA isolation and the determination of physiological properties.

4.7. Analyses of Physiological Parameters

The REL value was determined to evaluate the degree of stress damage in the transgenic tobacco plants following a previously reported protocol [69]. Briefly, 0.2 g of shredded leaves was placed in 20 mL distilled water to measure the electrolyte leakage (C1) after 24 h, and the electrolyte leakage of pure distilled water (C0) was also determined. The shredded leaves in the pure distilled water were boiled for 30 min, and then the electrolyte leakage was determined (C2). The relative electrolyte leakage was calculated with the formula REL = (C1 − C0)/(C2 − C0) × 100%.
For enzyme activity assay, the crude enzyme solution was produced by 0.2 g leaf samples powder in 5 mL sodium phosphate buffer at pH 7.8. The assay for determining the activity of SOD referred to Beauchamp and Fridovich, while POD, CAT, and APX activities were quantified as previous in research with a slight modification [70,71,72]. The assay for POD activity was modified by adding 0.1 mL enzyme solution to the substrate solution and determining the reaction mixture at A470 nm. The assay for CAT activity was performed by adding 0.2 mL enzyme solution into substrate solution and determining the reaction mixture at A240 nm. The assay for APX activity was revised as adding 0.2 mL enzyme solution into substrate solution and determining the reaction mixture at A290 nm. The reaction mixture of POD, CAT, and APX was determined every 30 s during a total 180 s reaction time, respectively.

5. Conclusions

In summary, this study identified 38 OfZAT genes, which could be classified into 5 subgroups based on phylogenetic relationships and sequence structures. The members of each subgroup contained similar motifs arranged in consistent patterns. In addition, 49 segmental and 5 tandem duplication events were detected among OfZATs and might have contributed to the expansion of the ZAT gene family. The ZAT genes predominantly contained cis-elements associated with hormone, stress, light, and developmental processes. Numerous OfZAT genes showed tissue-specific expression patterns. Screening of the transcriptome data revealed two genes that could be induced by salt stress. Under cold stress, eight genes were strongly and differently expressed, of which OfZAT35 showed a continuously increasing expression trend. OfZAT35 is located in the nucleus, and it showed no transcriptional activation activity. The transient overexpression of OfZAT35 in tobacco resulted in significantly higher REL values and downregulated the expression of positive to cold tolerance genes, such as NbDREB3, NbLEA5, and NbCAT, which suggested that OfZAT35 is a negative regulator of cold tolerance in transgenic tobacco. Overall, this study not only expands the understanding of the ZAT gene family in O. fragrans but also provides a basis for the further functional evaluation of OfZATs under cold stress.

Supplementary Materials

The following are available online at https://0-www-mdpi-com.brum.beds.ac.uk/article/10.3390/plants12122346/s1, Figure S1: Synteny analysis of ZAT gene family across the O. fragrans genome, Figure S2: The phylogenetic classification and motif composition of 89 ZAT genes, Figure S3: The cis-element screening in the promoter regions (2-kb genome sequence) of OfZATs, Figure S4: The expression profiles of OfZATsin the salt stress treatment (S0 h, S6 h, S24 h, S72 h) and control (S0 h, CK6 h, CK24 h, CK72 h), Figure S5: The expression profiles of OfZATs during cold stress treatment, Table S1: The Physicochemical Characteristics of OfZATs, Table S2: The sequences of 15 motifs in 89 ZATs, Table S3: The sequences of 15 motifs in OfZATs, Table S4: The FPKM values of OfZATs in different O. fragrans tissues, Table S5: The FPKM valus of OfZATs in the salt stress treatment and control, Table S6: The FPKM values of OfZATs during cold stress treatment, Table S7: Primer sequences for qRT-PCR and sqRT-PCR, Table S8: Primer sequences for qRT-PCR, Table S9: Primer sequences used for OfZAT35 amplification.

Author Contributions

Y.Y., X.Y. and L.W. designed the study; H.D., Z.Y., Z.Z. and K.F. conducted the experiments and analyzed the data; H.D. wrote the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the National Natural Science Foundation of China (Grant Nos. 32071828) and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

Data Availability Statement

All data in this study could be found in the manuscript or supplemental materials.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Wang, L.; Li, M.; Jin, W.; Li, S.; Zhang, S.; Yu, L. Variations in the components of Osmanthus fragrans Lour. essential oil at different stages of flowering. Food Chem. 2009, 114, 233–236. [Google Scholar] [CrossRef]
  2. Yue, Y.; Shi, T.; Liu, J.; Tian, Q.; Yang, X.; Wang, L. Genomic, metabonomic and transcriptomic analyses of sweet osmanthus varieties provide insights into floral aroma formation. Sci. Hortic. 2022, 306, 111442. [Google Scholar] [CrossRef]
  3. Chen, H.; Zeng, X.; Yang, J.; Cai, X.; Shi, Y.; Zheng, R.; Wang, Z.; Liu, J.; Yi, X.; Xiao, S.; et al. Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution. Hortic. Res. 2021, 8, 98. [Google Scholar] [CrossRef]
  4. Yang, X.; Yue, Y.; Li, H.; Ding, W.; Chen, G.; Shi, T.; Chen, J.; Park, M.S.; Chen, F.; Wang, L. The chromosome-level quality genome provides insights into the evolution of the biosynthesis genes for aroma compounds of Osmanthus fragrans. Hortic. Res. 2018, 5, 72. [Google Scholar] [CrossRef] [Green Version]
  5. Hung, C.Y.; Tsai, Y.C.; Li, K.Y. Phenolic antioxidants isolated from the flowers of Osmanthus fragrans. Molecules 2012, 17, 10724–10737. [Google Scholar] [CrossRef] [Green Version]
  6. Chen, X.; Yang, X.; Xie, J.; Ding, W.; Li, Y.; Yue, Y.; Wang, L. Biochemical and Comparative Transcriptome Analyses Reveal Key Genes Involved in Major Metabolic Regulation Related to Colored Leaf Formation in Osmanthus fragrans ‘Yinbi Shuanghui’ during Development. Biomolecules 2020, 10, 549. [Google Scholar] [CrossRef] [Green Version]
  7. Yue, Y.; Li, L.; Li, Y.; Li, H.; Ding, W.; Shi, T.; Chen, G.; Yang, X.; Wang, L. Genome-Wide Analysis of NAC Transcription Factors and Characterization of the Cold Stress Response in Sweet Osmanthus. Plant Mol. Biol. Rep. 2020, 38, 314–330. [Google Scholar] [CrossRef]
  8. Li, Y.; Li, L.; Ding, W.; Li, H.; Shi, T.; Yang, X.; Wang, L.; Yue, Y. Genome-wide identification of Osmanthus fragrans bHLH transcription factors and their expression analysis in response to abiotic stress. Environ. Exp. Bot. 2020, 172, 103990. [Google Scholar] [CrossRef]
  9. Bin, J.; Zhu, M.; Ding, H.; Zai, Z.; Shi, T.; Wang, L.; Yang, X.; Yue, Y. New Insights into the Roles of Osmanthus fragrans Heat-Shock Transcription Factors in Cold and Other Stress Responses. Horticulturae 2022, 8, 80. [Google Scholar] [CrossRef]
  10. Ritonga, F.N.; Ngatia, J.N.; Wang, Y.; Khoso, M.A.; Farooq, U.; Chen, S. AP2/ERF, an important cold stress-related transcription factor family in plants: A review. Physiol. Mol. Biol. Plants 2021, 27, 1953–1968. [Google Scholar] [CrossRef] [PubMed]
  11. Englbrecht, C.C.; Schoof, H.; Böhm, S. Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome. BMC Genom. 2004, 5, 39. [Google Scholar] [CrossRef] [Green Version]
  12. Xie, M.; Sun, J.; Gong, D.; Kong, Y. The Roles of Arabidopsis C1-2i Subclass of C2H2-type Zinc-Finger Transcription Factors. Genes 2019, 10, 653. [Google Scholar] [CrossRef] [Green Version]
  13. Cheuk, A.; Houde, M. Genome wide identification of C1-2i zinc finger proteins and their response to abiotic stress in hexaploid wheat. Mol. Genet. Genom. 2016, 291, 873–890. [Google Scholar] [CrossRef] [PubMed]
  14. Li, P.; Yu, A.; Sun, R.; Liu, A. Function and Evolution of C1-2i Subclass of C2H2-Type Zinc Finger Transcription Factors in POPLAR. Genes 2022, 13, 1843. [Google Scholar] [CrossRef] [PubMed]
  15. Kubo, K.-i.; Sakamoto, A.; Kobayashi, A.; Rybka, Z.; Kanno, Y.; Nakagawa, H.; Nishino, T.; Takatsuji, H. Cys2/His2 zinc-finger protein family of petunia: Evolution and general mechanism of target-sequence recognition. Nucleic Acids Res. 1998, 26, 608–615. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  16. Rehman, A.; Wang, N.; Peng, Z.; He, S.; Zhao, Z.; Gao, Q.; Wang, Z.; Li, H.; Du, X. Identification of C2H2 subfamily ZAT genes in Gossypium species reveals GhZAT34 and GhZAT79 enhanced salt tolerance in Arabidopsis and cotton. Int. J. Biol. Macromol. 2021, 184, 967–980. [Google Scholar] [CrossRef]
  17. Li, H.; Yue, M.; Jiang, L.; Liu, Y.; Zhang, N.; Liu, X.; Ye, Y.; Lin, X.; Zhang, Y.; Lin, Y.; et al. Genome-Wide Identification of Strawberry C2H2-ZFP C1-2i Subclass and the Potential Function of FaZAT10 in Abiotic Stress. Int. J. Mol. Sci. 2022, 23, 13079. [Google Scholar] [CrossRef]
  18. Ciftci-Yilmaz, S.; Mittler, R. The zinc finger network of plants. Cell Mol. Life Sci. 2008, 65, 1150–1160. [Google Scholar] [CrossRef]
  19. Wang, H.; Zou, Z.; Wang, S.; Gong, M. Global analysis of transcriptome responses and gene expression profiles to cold stress of Jatropha curcas L. PLoS ONE 2013, 8, e82817. [Google Scholar] [CrossRef]
  20. Min, X.; Liu, Z.; Wang, Y.; Liu, W. Comparative transcriptomic analysis provides insights into the coordinated mechanisms of leaves and roots response to cold stress in Common Vetch. Ind. Crops Prod. 2020, 158, 112949. [Google Scholar] [CrossRef]
  21. Xu, J.; Chen, Z.; Wang, F.; Jia, W.; Xu, Z. Combined transcriptomic and metabolomic analyses uncover rearranged gene expression and metabolite metabolism in tobacco during cold acclimation. Sci. Rep. 2020, 10, 5242. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  22. Fu, J.; Wan, L.; Song, L.; He, L.; Jiang, N.; Long, H.; Huo, J.; Ji, X.; Hu, F.; Wei, S.; et al. A De Novo Transcriptome Analysis Identifies Cold-Responsive Genes in the Seeds of Taxillus chinensis (DC.) Danser. Biomed. Res. Int. 2022, 2022, 9247169. [Google Scholar] [CrossRef] [PubMed]
  23. Peng, T.; You, X.; Guo, L.; Zhong, B.; Mi, L.; Chen, J.; Xiao, X. Transcriptome analysis of Chongyi wild mandarin, a wild species more cold-tolerant than Poncirus trifoliata, reveals key pathways in response to cold. Environ. Exp. Bot. 2021, 184, 104371. [Google Scholar] [CrossRef]
  24. Ke, L.; Lei, W.; Yang, W.; Wang, J.; Gao, J.; Cheng, J.; Sun, Y.; Fan, Z.; Yu, D. Genome-wide identification of cold responsive transcription factors in Brassica napus L. BMC Plant Biol. 2020, 20, 62. [Google Scholar] [CrossRef] [PubMed]
  25. Ciftci-Yilmaz, S.; Morsy, M.R.; Song, L.; Coutu, A.; Krizek, B.A.; Lewis, M.W.; Warren, D.; Cushman, J.; Connolly, E.L.; Mittler, R. The EAR-motif of the Cys2/His2-type zinc finger protein Zat7 plays a key role in the defense response of Arabidopsis to salinity stress. J. Biol. Chem. 2007, 282, 9260–9268. [Google Scholar] [CrossRef] [Green Version]
  26. Sakamoto, H.; Maruyama, K.; Sakuma, Y.; Meshi, T.; Iwabuchi, M.; Shinozaki, K.; Yamaguchi-Shinozaki, K. Arabidopsis Cys2/His2-type zinc-finger proteins function as transcription repressors under drought, cold, and high-salinity stress conditions. Plant Physiol. 2004, 136, 2734–2746. [Google Scholar] [CrossRef] [Green Version]
  27. Liu, Y.; Khan, A.R.; Gan, Y. C2H2 Zinc Finger Proteins Response to Abiotic Stress in Plants. Int. J. Mol. Sci. 2022, 23, 2730. [Google Scholar] [CrossRef]
  28. Lee, H.; Guo, Y.; Ohta, M.; Xiong, L.; Stevenson, B.; Zhu, J.K. LOS2, a genetic locus required for cold-responsive gene transcription encodes a bi-functional enolase. EMBO J. 2002, 21, 2692–2702. [Google Scholar] [CrossRef]
  29. Doherty, C.J.; Van Buskirk, H.A.; Myers, S.J.; Thomashow, M.F. Roles for Arabidopsis CAMTA transcription factors in cold-regulated gene expression and freezing tolerance. Plant Cell 2009, 21, 972–984. [Google Scholar] [CrossRef] [Green Version]
  30. Jaglo-Ottosen, K.R.; Gilmour, S.J.; Zarka, D.G.; Schabenberger, O.; Thomashow, M.F. Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance. Science 1998, 280, 104–106. [Google Scholar] [CrossRef] [Green Version]
  31. Vogel, J.T.; Zarka, D.G.; Van Buskirk, H.A.; Fowler, S.G.; Thomashow, M.F. Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis. Plant J. 2005, 41, 195–211. [Google Scholar] [CrossRef]
  32. Zhu, M.; Bin, J.; Ding, H.; Pan, D.; Tian, Q.; Yang, X.; Wang, L.; Yue, Y. Insights into the trihelix transcription factor responses to salt and other stresses in Osmanthus fragrans. BMC Genom. 2022, 23, 334. [Google Scholar] [CrossRef]
  33. Zhao, H.; Lou, Y.; Sun, H.; Li, L.; Wang, L.; Dong, L.; Gao, Z. Transcriptome and comparative gene expression analysis of Phyllostachys edulis in response to high light. BMC Plant Biol. 2016, 16, 34. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  34. Bajji, M.; Kinet, J.-M.; Lutts, S. The use of the electrolyte leakage method for assessing cell membrane stability as a water stress tolerance test in durum wheat. Plant Growth Regul. 2002, 36, 61–70. [Google Scholar] [CrossRef]
  35. Filek, M.; Walas, S.; Mrowiec, H.; Rudolphy-Skórska, E.; Sieprawska, A.; Biesaga-Kościelniak, J. Membrane permeability and micro- and macroelement accumulation in spring wheat cultivars during the short-term effect of salinity- and PEG-induced water stress. Acta Physiol. Plant. 2011, 34, 985–995. [Google Scholar] [CrossRef] [Green Version]
  36. Chen, G.; Liu, Z.; Li, S.; Qanmber, G.; Liu, L.; Guo, M.; Lu, L.; Ma, S.; Li, F.; Yang, Z. Genome-wide analysis of ZAT gene family revealed GhZAT6 regulates salt stress tolerance in G. hirsutum. Plant Sci. 2021, 312, 111055. [Google Scholar] [CrossRef]
  37. Vision, T.J.; Brown, D.G.; Tanksley, S.D. The origins of genomic duplications in Arabidopsis. Science 2000, 290, 2114–2117. [Google Scholar] [CrossRef] [Green Version]
  38. Chu, C.; Sun, M.; Wu, Y.; Yan, Z.; Li, T.; Feng, Y.; Guo, Y.; Yin, T.; Xue, L. Pan-genome and genomic variation analyses of Populus. J. Nanjin For. Univ. 2022, 46, 251–260. [Google Scholar]
  39. Dudhate, A.; Shinde, H.; Yu, P.; Tsugama, D.; Gupta, S.K.; Liu, S.; Takano, T. Comprehensive analysis of NAC transcription factor family uncovers drought and salinity stress response in pearl millet (Pennisetum glaucum). BMC Genom. 2021, 22, 70. [Google Scholar] [CrossRef]
  40. Cannon, S.B.; Mitra, A.; Baumgarten, A.; Young, N.D.; May, G. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol. 2004, 4, 10. [Google Scholar] [CrossRef] [Green Version]
  41. Jeffares, D.C.; Penkett, C.J.; Bahler, J. Rapidly regulated genes are intron poor. Trends Genet. 2008, 24, 375–378. [Google Scholar] [CrossRef]
  42. Liu, J.; Peng, T.; Dai, W. Critical cis-Acting Elements and Interacting Transcription Factors: Key Players Associated with Abiotic Stress Responses in Plants. Plant Mol. Bio. Rep. 2013, 32, 303–317. [Google Scholar] [CrossRef]
  43. Illgen, S.; Zintl, S.; Zuther, E.; Hincha, D.K.; Schmulling, T. Characterisation of the ERF102 to ERF105 genes of Arabidopsis thaliana and their role in the response to cold stress. Plant Mol. Biol. 2020, 103, 303–320. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  44. Han, G.; Lu, C.; Guo, J.; Qiao, Z.; Sui, N.; Qiu, N.; Wang, B. C2H2 Zinc Finger Proteins: Master Regulators of Abiotic Stress Responses in Plants. Front. Plant Sci. 2020, 11, 115. [Google Scholar] [CrossRef] [Green Version]
  45. Kim, S.H.; Hong, J.K.; Lee, S.C.; Sohn, K.H.; Jung, H.W.; Hwang, B.K. CAZFP1, Cys2/His2-type zinc-finger transcription factor gene functions as a pathogen-induced early-defense gene in Capsicum annuum. Plant Mol. Biol. 2004, 55, 883–904. [Google Scholar] [CrossRef]
  46. Gamsjaeger, R.; Liew, C.K.; Loughlin, F.E.; Crossley, M.; Mackay, J.P. Sticky fingers: Zinc-fingers as protein-recognition motifs. Trends Biochem. Sci. 2007, 32, 63–70. [Google Scholar] [CrossRef] [PubMed]
  47. Brayer, K.J.; Kulshreshtha, S.; Segal, D.J. The Protein-Binding Potential of C2H2 Zinc Finger Domains. Cell Biochem. Biophys. 2008, 51, 9–19. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  48. Kovaleski, A.P.; Grossman, J.J. Standardization of electrolyte leakage data and a novel liquid nitrogen control improve measurements of cold hardiness in woody tissue. Plant Methods 2021, 17, 53. [Google Scholar] [CrossRef]
  49. Dong, H.; Wu, C.; Luo, C.; Wei, M.; Qu, S.; Wang, S. Overexpression of MdCPK1a gene, a calcium dependent protein kinase in apple, increase tobacco cold tolerance via scavenging ROS accumulation. PLoS ONE 2020, 15, e0242139. [Google Scholar] [CrossRef]
  50. Luo, P.; Li, Z.; Chen, W.; Xing, W.; Yang, J.; Cui, Y. Overexpression of RmICE1, a bHLH transcription factor from Rosa multiflora, enhances cold tolerance via modulating ROS levels and activating the expression of stress-responsive genes. Environ. Exp. Bot. 2020, 178, 104160. [Google Scholar] [CrossRef]
  51. Xu, S.; Li, Y.; Hu, J.; Guan, Y.; Ma, W.; Zheng, Y.; Zhu, S. Responses of Antioxidant Enzymes to Chilling Stress in Tobacco Seedlings. Agric. Sci. China 2010, 9, 1594–1601. [Google Scholar] [CrossRef]
  52. Matsumura, T.; Tabayashi, N.; Kamagata, Y.; Souma, C.; Saruyama, H. Wheat catalase expressed in transgenic rice can improve tolerance against low temperature stress. Physiol. Plantarum. 2002, 116, 317–327. [Google Scholar] [CrossRef]
  53. Geng, J.; Wei, T.; Wang, Y.; Huang, X.; Liu, J.H. Overexpression of PtrbHLH, a basic helix-loop-helix transcription factor from Poncirus trifoliata, confers enhanced cold tolerance in pummelo (Citrus grandis) by modulation of H2O2 level via regulating a CAT gene. Tree Physiol. 2019, 39, 2045–2054. [Google Scholar] [CrossRef]
  54. Thomashow, M.F. Molecular basis of plant cold acclimation: Insights gained from studying the CBF cold response pathway. Plant Physiol. 2010, 154, 571–577. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  55. Qiu, H.; Zhang, L.; Liu, C.; He, L.; Wang, A.; Liu, H.; Zhu, J. Cloning and characterization of a novel dehydrin gene, SiDhn2, from Saussurea involucrata Kar. et Kir. Plant Mol. Biol. 2014, 84, 707–718. [Google Scholar] [CrossRef]
  56. Kang, J.; Zhang, H.; Sun, T.; Shi, Y.; Wang, J.; Zhang, B.; Wang, Z.; Zhou, Y.; Gu, H. Natural variation of C-repeat-binding factor (CBFs) genes is a major cause of divergence in freezing tolerance among a group of Arabidopsis thaliana populations along the Yangtze River in China. New Phytol. 2013, 199, 1069–1080. [Google Scholar] [CrossRef]
  57. Finn, R.D.; Clements, J.; Eddy, S.R. HMMER web server: Interactive sequence similarity searching. Nucleic Acids Res. 2011, 39, W29–W37. [Google Scholar] [CrossRef] [Green Version]
  58. Wilkins, M.R. Protein identification and analysis tools in the ExPASy server. Methods Mol. Biol. 1999, 112, 531–552. [Google Scholar] [PubMed]
  59. Horton, P.; Park, K.-J.; Obayashi, T.; Fujita, N.; Harada, H.; Adams-Collier, C.; Nakai, K. WoLF PSORT: Protein localization predictor. Nucleic Acids Res. 2007, 35, W585–W587. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  60. Kumar, S.; Tamura, K.; Nei, M. MEGA: Molecular evolutionary genetics analysis software for microcomputers. Bioinformatics 1994, 10, 189–191. [Google Scholar] [CrossRef] [Green Version]
  61. Wang, Y.; Tang, H.; DeBarry, J.D.; Tan, X.; Li, J.; Wang, X.; Lee, T.; Jin, H.; Marler, B.; Guo, H. MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012, 40, e49. [Google Scholar] [CrossRef] [Green Version]
  62. Chen, C.; Wu, Y.; Xia, R. A painless way to customize Circos plot: From data preparation to visualization using TBtools. iMeta 2022, 1, e35. [Google Scholar] [CrossRef]
  63. Chen, C.; Chen, H.; Zhang, Y.; Thomas, H.R.; Frank, M.H.; He, Y.; Xia, R. TBtools: An integrative toolkit developed for interactive analyses of big biological data. Mol. Plant 2020, 13, 1194–1202. [Google Scholar] [CrossRef]
  64. Bailey, T.L.; Boden, M.; Buske, F.A.; Frith, M.; Grant, C.E.; Clementi, L.; Ren, J.Y.; Li, W.W.; Noble, W.S. MEME SUITE: Tools for motif discovery and searching. Nucleic Acids Res. 2009, 37 (Supp1. 2), W202–W208. [Google Scholar] [CrossRef] [PubMed]
  65. Lescot, M.; Déhais, P.; Thijs, G.; Marchal, K.; Moreau, Y.; Van de Peer, Y.; Rouzé, 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 Res. 2002, 30, 325–327. [Google Scholar] [CrossRef]
  66. Lalitha, S. Primer premier 5. Biotech Softw. Internet Rep. Comput. Software. J. Sci. 2000, 1, 270–272. [Google Scholar] [CrossRef]
  67. Zhang, C.; Fu, J.; Wang, Y.; Bao, Z.; Zhao, H. Identification of Suitable Reference Genes for Gene Expression Normalization in the Quantitative Real-Time PCR Analysis of Sweet Osmanthus (Osmanthus fragrans Lour.). PLoS ONE 2015, 10, e0136355. [Google Scholar] [CrossRef] [Green Version]
  68. Yu, P.; Shinde, H.; Dudhate, A.; Tsugama, D.; Gupta, S.K.; Liu, S.; Takano, T. Genome-wide investigation of SQUAMOSA promoter binding protein-like transcription factor family in pearl millet (Pennisetum glaucum (L.) R. Br.). Plant Gene 2021, 27, 100313. [Google Scholar] [CrossRef]
  69. Campos, P.S.; Quartin, V.; Ramalho, J.C.; Nunes, M.A. Electrolyte leakage and lipid degradation account for cold sensitivity in leaves of Coffea sp. plants. J. Plant Physiol. 2003, 160, 283–292. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  70. Lin, S.; Zhang, Z.-Y.; Liu, W.-F.; Lin, Y.-Z.; Zhang, Q.; Zhu, B.-Q. Role of glucose-6-phosphate dehydrogenase in freezing-induced freezing resistance of Populus suaveolens. Plant Physiol. J. 2005, 31, 34–40. [Google Scholar]
  71. Liu, Y.; Yang, X.; Zhu, S.; Wang, Y. Postharvest application of MeJA and NO reduced chilling injury in cucumber (Cucumis sativus) through inhibition of H2O2 accumulation. Postharvest Biol. Technol. 2016, 119, 77–83. [Google Scholar] [CrossRef]
  72. Nakano, Y.; Asada, K. Hydrogen Peroxide is Scavenged by Ascorbate-specific Peroxidase in Spinach Chloroplasts. Plant Cell Physiol. 1981, 22, 867–880. [Google Scholar]
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Figure 1. Chromosome distribution of OfZAT genes in the O. fragrans genome. The serial numbers of chromosomes are listed in blue on the left of each chromosome. The names of genes are listed on the right of each chromosome in red, and the genes with orange background originated from tandem duplication.
Figure 1. Chromosome distribution of OfZAT genes in the O. fragrans genome. The serial numbers of chromosomes are listed in blue on the left of each chromosome. The names of genes are listed on the right of each chromosome in red, and the genes with orange background originated from tandem duplication.
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Figure 2. Evolutionary relationship of ZAT genes in sweet osmanthus (O. fragrans), Arabidopsis (A. thaliana), rice (O. sativa), and black cottonwood (P. trichocarpa) constructed using the NJ method. The values indicated 1000 bootstrap replication supports. The ZAT genes were classified into five subgroups that are highlighted in different colors.
Figure 2. Evolutionary relationship of ZAT genes in sweet osmanthus (O. fragrans), Arabidopsis (A. thaliana), rice (O. sativa), and black cottonwood (P. trichocarpa) constructed using the NJ method. The values indicated 1000 bootstrap replication supports. The ZAT genes were classified into five subgroups that are highlighted in different colors.
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Figure 3. The phylogenetic classification, gene structure, and motif composition of OfZATs. (a) The phylogenetic trees of OfZATs showing different subgroups are marked with different colors. (b) Conserved motifs in OfZATs are highlighted in different colors. (c) The gene structures of OfZATs showing introns and exons. The yellow, green, and grey line regions represent conserved domains, CDS, and introns, respectively.
Figure 3. The phylogenetic classification, gene structure, and motif composition of OfZATs. (a) The phylogenetic trees of OfZATs showing different subgroups are marked with different colors. (b) Conserved motifs in OfZATs are highlighted in different colors. (c) The gene structures of OfZATs showing introns and exons. The yellow, green, and grey line regions represent conserved domains, CDS, and introns, respectively.
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Figure 4. The temporal and spatial expression profiles of OfZATs in different O. fragrans tissues. The hierarchically clustered heat map was constructed using the FPKM values from transcriptome data converted to log2 (FPKM value + 1). The original FPKM values are shown in the heat map. The column legend on the right stands for the color of log2 (FPKM value + 1) in the heat map.
Figure 4. The temporal and spatial expression profiles of OfZATs in different O. fragrans tissues. The hierarchically clustered heat map was constructed using the FPKM values from transcriptome data converted to log2 (FPKM value + 1). The original FPKM values are shown in the heat map. The column legend on the right stands for the color of log2 (FPKM value + 1) in the heat map.
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Figure 5. The expression profiles of four OfZATs (OfZAT8/25/35/36) in the salt stress treatment (S0 h, S6 h, S24 h, S72 h) and control (S0 h, CK6 h, CK24 h, CK72 h). The hierarchically clustered heat map was constructed using the FPKM values converted to log2 (FPKM value + 1). The original FPKM values are shown in the heat map. The column legend on the right stands for the color of log2 (FPKM value + 1) in the heat map.
Figure 5. The expression profiles of four OfZATs (OfZAT8/25/35/36) in the salt stress treatment (S0 h, S6 h, S24 h, S72 h) and control (S0 h, CK6 h, CK24 h, CK72 h). The hierarchically clustered heat map was constructed using the FPKM values converted to log2 (FPKM value + 1). The original FPKM values are shown in the heat map. The column legend on the right stands for the color of log2 (FPKM value + 1) in the heat map.
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Figure 6. The expression profiles of nine OfZATs (OfZAT7/8/25/26/29/32/35/36/38) during cold stress treatment. The six periods during cold treatment were represented as C0 h, C3 h, C12 h, C24 h, C72 h, and C120 h. Cr72 h represented recovering 72 h after cold treatment. The hierarchically clustered heat map was constructed using the FPKM values converted to log2 (FPKM value + 1). The original FPKM values are shown in the heat map. The column legend on the right stands for the color of log2 (FPKM value + 1) in the heat map.
Figure 6. The expression profiles of nine OfZATs (OfZAT7/8/25/26/29/32/35/36/38) during cold stress treatment. The six periods during cold treatment were represented as C0 h, C3 h, C12 h, C24 h, C72 h, and C120 h. Cr72 h represented recovering 72 h after cold treatment. The hierarchically clustered heat map was constructed using the FPKM values converted to log2 (FPKM value + 1). The original FPKM values are shown in the heat map. The column legend on the right stands for the color of log2 (FPKM value + 1) in the heat map.
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Figure 7. The relative expression levels of five selected OfZATs during cold treatment. The histograms indicating the data from qRT-PCR and FPKM values from transcription data are marked by a red line. The qRT-PCR data were statistically assessed using one-way ANOVA followed by Duncan’s test (p < 0.05), and the error bar represents ± SE (standard error) (n = 3). The letters (a, b, c) indicated the statistically differences based on Duncan’s test (p < 0.05).
Figure 7. The relative expression levels of five selected OfZATs during cold treatment. The histograms indicating the data from qRT-PCR and FPKM values from transcription data are marked by a red line. The qRT-PCR data were statistically assessed using one-way ANOVA followed by Duncan’s test (p < 0.05), and the error bar represents ± SE (standard error) (n = 3). The letters (a, b, c) indicated the statistically differences based on Duncan’s test (p < 0.05).
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Figure 8. Subcellular localization assay and transcriptional activation activity of OfZAT35. (a) The subcellular location of OfZAT35. DAPI (4′,6-diamidino-2-phenylindole) was utilized to mark the nuclei florescent signals in the epidermal cells of tobacco. (b) The transcriptional activation activity of OfZAT35. The empty PGBKT7 vector (negative control) and recombinant plasmids pGBKT7-OfZAT35 were transformed into yeast strain AH109. The yeast strain of negative control and OfZAT35 (pGBKT7-OfZAT35) grew on different screening culture media (SD/-Trp, SD/-Trp-Ade, and SD/-Trp-Ade + X-α-gal medium). The number of 100, 10−1, 10−2, 10−3, and 10−4 represents the concentration of dilution ratio of original yeast culture.
Figure 8. Subcellular localization assay and transcriptional activation activity of OfZAT35. (a) The subcellular location of OfZAT35. DAPI (4′,6-diamidino-2-phenylindole) was utilized to mark the nuclei florescent signals in the epidermal cells of tobacco. (b) The transcriptional activation activity of OfZAT35. The empty PGBKT7 vector (negative control) and recombinant plasmids pGBKT7-OfZAT35 were transformed into yeast strain AH109. The yeast strain of negative control and OfZAT35 (pGBKT7-OfZAT35) grew on different screening culture media (SD/-Trp, SD/-Trp-Ade, and SD/-Trp-Ade + X-α-gal medium). The number of 100, 10−1, 10−2, 10−3, and 10−4 represents the concentration of dilution ratio of original yeast culture.
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Figure 9. Physiological and biochemical analysis of transiently transformed tobacco. The data were statistically assessed using Duncan’s test (* p < 0.05). (a) The sqRT-PCR analysis of transiently transformed tobacco of OfZAT35 and EV. The Nbactin was selected as a reference gene. L1−3 represent three transiently transformed tobacco lines of EV, while L4−6 represent transiently transformed lines of OfZAT35. (b) The analysis of REL in cold stress treated tobacco. (c) qRT-PCR analysis of ROS (reactive oxygen species) and cold-stress-related genes. (d) Analysis of SOD, POD, CAT, and APX antioxidant enzyme activities.
Figure 9. Physiological and biochemical analysis of transiently transformed tobacco. The data were statistically assessed using Duncan’s test (* p < 0.05). (a) The sqRT-PCR analysis of transiently transformed tobacco of OfZAT35 and EV. The Nbactin was selected as a reference gene. L1−3 represent three transiently transformed tobacco lines of EV, while L4−6 represent transiently transformed lines of OfZAT35. (b) The analysis of REL in cold stress treated tobacco. (c) qRT-PCR analysis of ROS (reactive oxygen species) and cold-stress-related genes. (d) Analysis of SOD, POD, CAT, and APX antioxidant enzyme activities.
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MDPI and ACS Style

Ding, H.; Yang, Z.; Zai, Z.; Feng, K.; Wang, L.; Yue, Y.; Yang, X. Genome-Wide Analysis of ZAT Gene Family in Osmanthus fragrans and the Function Exploration of OfZAT35 in Cold Stress. Plants 2023, 12, 2346. https://0-doi-org.brum.beds.ac.uk/10.3390/plants12122346

AMA Style

Ding H, Yang Z, Zai Z, Feng K, Wang L, Yue Y, Yang X. Genome-Wide Analysis of ZAT Gene Family in Osmanthus fragrans and the Function Exploration of OfZAT35 in Cold Stress. Plants. 2023; 12(12):2346. https://0-doi-org.brum.beds.ac.uk/10.3390/plants12122346

Chicago/Turabian Style

Ding, Huifen, Zhandong Yang, Zhouying Zai, Keyi Feng, Lianggui Wang, Yuanzheng Yue, and Xiulian Yang. 2023. "Genome-Wide Analysis of ZAT Gene Family in Osmanthus fragrans and the Function Exploration of OfZAT35 in Cold Stress" Plants 12, no. 12: 2346. https://0-doi-org.brum.beds.ac.uk/10.3390/plants12122346

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