Next Article in Journal
Towards Precision Prognostication and Personalized Therapeutics through Proteomics
Next Article in Special Issue
Salinity-Triggered Responses in Plant Apical Meristems for Developmental Plasticity
Previous Article in Journal
Determination of Selected Isoquinoline Alkaloids from Chelidonium majus, Mahonia aquifolium and Sanguinaria canadensis Extracts by Liquid Chromatography and Their In Vitro and In Vivo Cytotoxic Activity against Human Cancer Cells
Previous Article in Special Issue
Lactate Dehydrogenase Superfamily in Rice and Arabidopsis: Understanding the Molecular Evolution and Structural Diversity
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
IJMS
Volume 24
Issue 7
10.3390/ijms24076359
ijms-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Genomic Identification of CCCH-Type Zinc Finger Protein Genes Reveals the Role of HuTZF3 in Tolerance of Heat and Salt Stress of Pitaya (Hylocereus polyrhizus)

by
Weijuan Xu
1,2,
Shuguang Jian
3,4,
Jianyi Li
1,2,
Yusang Wang
5,
Mingyong Zhang
1,3,* and
Kuaifei Xia
1,3,*
1
Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
2
University of Chinese Academy of Sciences, Beijing 100049, China
3
South China National Botanical Garden, Guangzhou 510650, China
4
CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
5
College of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2023, 24(7), 6359; https://doi.org/10.3390/ijms24076359
Submission received: 14 February 2023 / Revised: 14 March 2023 / Accepted: 21 March 2023 / Published: 28 March 2023
(This article belongs to the Special Issue Molecular Aspects of Plant Salinity Stress and Tolerance 2.0)
Browse Figures
Versions Notes

Abstract

:
Pitaya (Hylocereus polyrhizus) is cultivated in a broad ecological range, due to its tolerance to drought, heat, and poor soil. The zinc finger proteins regulate gene expression at the transcriptional and post-transcriptional levels, by interacting with DNA, RNA, and proteins, to play roles in plant growth and development, and stress response. Here, a total of 81 CCCH-type zinc finger protein genes were identified from the pitaya genome. Transcriptomic analysis showed that nine of them, including HuTZF3, responded to both salt and heat stress. RT-qPCR results showed that HuTZF3 is expressed in all tested organs of pitaya, with a high level in the roots and stems, and confirmed that expression of HuTZF3 is induced by salt and heat stress. Subcellular localization showed that HuTZF3 is targeted in the processing bodies (PBs) and stress granules (SGs). Heterologous expression of HuTZF3 could improve both salt and heat tolerance in Arabidopsis, reduce oxidative stress, and improve the activity of catalase and peroxidase. Therefore, HuTZF3 may be involved in post-transcriptional regulation via localizing to PBs and SGs, contributing to both salt and heat tolerance in pitaya.

1. Introduction

Soil salinity and increasing temperature caused by human activities, are two major environmental factors affecting plant growth and production [1,2]. To face salt and heat stress, plants initiate a series of physiological and biochemical reactions, to reduce damage and maintain adequate growth [3]. Pitaya (dragon fruit) is one of the tropical fruits belonging to the genus Hylocereus, in the Cactaceae family, with high commercial and medical value [4]. Pitaya is cultivated in a broad ecological range, due to its tolerance to drought, heat, and poor soil [5,6]. Pitaya performs crassulacean acid metabolism (CAM)-type photosynthesis [7], and its stems have spines and no leaves. Pitaya, like other CAM plants, has high water-use efficiency, due to the unique stomatal regulation pattern. The stomata of CAM plants open for CO2 uptake and fixing at night with lower temperature and higher humidity, and close for reducing water loss in the daytime when the stored CO2 is re-fixed by Rubisco for sugar synthesis [8,9,10]. So, CAM plants can endure various stresses including drought, salinity, and heat, and successfully survival in various ecological habitats, from deserts to forests [11].
There are many studies at transcriptomic and proteomic levels exploring the molecular mechanism in pitaya response to abiotic stresses including drought, salt, cold, and heat [5,6,12,13]. The pitaya catalase gene HuCAT3, is induced by H2O2, cold, drought, and salt stress, and plays an essential role in pitaya’s abiotic stress tolerance [14]. HuERF1 is induced by salt stress and participates in the ethylene-mediated salt tolerance of pitaya [15]. The pitaya miR396b is involved in response to drought, cold, heat, salt, and abscisic acid (ABA), by regulating its target gene HpGRF6 [16]. HuPR-1, a pathogenesis-related protein 1, is induced by heat stress, and overexpressing HuPR-1 improved Arabidopsis heat tolerance [6]. The genome of pitaya has been sequenced, it is diploid (2n = 22 chromosomes) [17]. However, little is known about the genes responding to both salt and heat stress in pitaya.
The zinc finger proteins are a large class of transcription factors containing zinc finger domains, and regulate gene expression at the transcriptional and post-transcriptional levels by interacting with DNA, RNA, and proteins, and then play important roles in plant growth and development, and stress response [18]. The number and arrangement of Cys and His residues in the zinc finger proteins, can be divided into nine categories, including C2H2, C2HC, C2HC5, CCCH, C3HC4, C4, C4HC3, C6, and C8 [19,20]. Among them, the CCCH-type zinc finger proteins usually contain 1–6 copies of CCCH-type motifs of C-X4-15-C-X4-6-C-X3-4-H (X represents other amino acids). Tandem CCCH zinc finger (TZF) protein contains two CCCH motifs in tandem. The plant TZF protein contains a plant-unique arginine-rich (RR) motif (C-X7–8-C-X5-C-X3) in the front of the TZF motif [21,22]. Plant TZF proteins are further divided into two groups: the RR-TZF group, containing the arginine-rich (RR) and TZF domains, and the ANK-RR-TZF group, containing the Ankyrin repeat (ANK) and RR-TZF domains [21]. The ANK repeat motif is known as a protein–protein interaction motif and plays a role in plant growth and development [23]. Both RR and TZF domains can bind RNA, leading to the critical role of TZFs in regulating RNA metabolism [24].
Most TZFs are RNA binding proteins involved in RNA regulation, and localized to processing bodies (PBs) and stress granules (SGs). PBs and SGs are two cytoplasmic mRNP granules containing messenger ribonucleoprotein, and play important roles in post-transcriptional and translational levels. PBs are involved in mRNA decay, while SGs hinder translation initiation, but allow elongation [25,26]. AtTZF1/AtC3H23 can regulate gene expression at the RNA level by binding RNA, and participate in flowering, cold, and drought tolerance [27,28]. AtTZF2/AtC3H20 and AtTZF3/AtC3H49 have RNase activity in vitro, to promote the degradation of target mRNAs, and participate in RNA metabolism [29]. OsTZF1 affects RNA stability via binding mRNA containing the AU-rich motif in 3‘UTR, to delay senescence and improve plant stress tolerance [30]. OsTZF7 is localized to PBs and SGs, and downregulates target gene expression by binding the ARE motif in the mRNA 3′UTR region, to enhance drought tolerance in rice [31].
In this study, we analyzed the response of HuTZF3 and the CCCH genes family of pitaya, to salt and heat stress. A total of 81 CCCH genes were identified from the pitaya genome, and the expression of nine of the genes responds to both salt and heat stress. Heterologous expression of HuTZF3 could improve the tolerance of Arabidopsis to both salt and heat stress, and HuTZF3 is localized in PBs and SGs. Therefore, we deduced that HuTZF3 might affect RNA stability, to mediate the salt and heat tolerance.

2. Results

2.1. Identification of the CCCH-Type Zinc Finger Protein Genes from Pitaya

To identify the CCCH-type zinc finger protein genes from pitaya, the Pitaya Genomic Database was searched, and the CCCH zinc finger domain was confirmed in SMART, NCBI conserved domain search tools, and the Pfam database. A total of 81 CCCH-type zinc finger protein genes (HuCCCHs) were obtained (Figure 1 and Supplementary Table S1), and they were randomly distributed on the 11 chromosomes of pitaya (Figure 1A). These HuCCCHs were named from HuCCCH1 to HuCCCH81, based on their chromosomal location, and their information is listed in Supplementary Table S1. In order to investigate their phylogenetic relationship, we constructed a phylogenetic tree with the CCCH-type zinc finger proteins from pitaya and Arabidopsis (Figure 1B). The pitaya HuCCCH proteins could be divided into 11 subfamilies, like those of Arabidopsis.
Since HuTZF3 belongs to subfamily IX of the HuCCCH family (Figure 1B), we analyzed the conserved motif, conserved domain, cis-elements in promoter, and gene structure of the 16 TZF-type zinc finger protein genes in the subfamily IX (Supplementary Figure S1 and Table S3). The promoter cis-element analysis showed that there are many cis-elements in the promoter of HuTZFs, such as plant growth and development, hormone, and abiotic stress-related cis-elements (Supplementary Figure S1B). According to the phylogenetic tree, conserved motif, and conserved domain, the 16 pitaya TZF proteins were divided into two groups: the RR-TZF group, including HuTZF1-10, and the ANK-RR-TZF group, including HuTZF11-16, similar to that of Arabidopsis (Supplementary Figure S2). All HuTZFs of the subfamily IX have the RR-TZF domain, that the RR (arginine-rich) domain localized in front of the TZF domain (Supplementary Figure S2A). HuTZF11-16 contains the ANK (Ankyrin repeat) domain and the RR-TZF domain belongs to the ANK-RR-TZF group (Supplementary Figure S2B).

2.2. Identification of HuCCCHs Response to Heat and Salt Stress

To screen which HuCCCHs respond to both heat and salt stress, we analyzed our previous transcriptomic data of pitaya seedlings under salt and heat treatment [5,6]. We found that sixteen of the HuCCCHs responded to heat treatment (Figure 2A), and 26 genes responded to salt treatment (Figure 2B). Among them, nine genes were induced by both salt and heat stress, and they are HuTZFs3/4/12 and C3H31/32/39/40/54/67. To verify this result, the expression pattern of HuTZF3 was analyzed in different tissues and response to salt and heat stress by RT-qPCR (Figure 2C–E). The results showed that expression of HuTZF3 was detected in different tissues. HuTZF3 had a high expression level in roots and stems, and a low expression level in petal and calyx (Figure 2C). The expression of HuTZF3 gradually increased under salt stress (Figure 2D), and its expression was rapidly induced by heat stress and reached a peak at 3 h (Figure 2E), which confirmed the screening result above from the transcriptomic data [5,6].

2.3. Heterologous Expression of HuTZF3 Improved Salt and Heat Tolerance in Arabidopsis

To study whether HuTZF3 affects the salt and heat tolerance of plants, we heterologously expressed HuTZF3 in Arabidopsis with CaMV35S promoter (Figure 3). Three independent homozygous HuTZF3 overexpressing lines (OE-4/14/17), showed high expression of HuTZF3 (Figure 3C), and were selected for further study. First, the salt tolerance of these transgenic Arabidopsis was tested under different concentrations of NaCl, using the seedlings. When the five-day-old seedlings were transferred to MS medium, containing 0, 100, 150, and 200 mM NaCl, and then cultured for 7 days, the root length of the OE lines was significantly longer than that of the wild type (WT); however, there was no significant difference between the WT and OE lines when they were grown on MS without NaCl (Figure 3A,B). When the four-week-old Arabidopsis of the WT and OE lines were grown in soil and then subjected to 300 mM NaCl, the OE lines also showed a higher survival rate to salt stress than the WT (Figure 3D,E).
The heat tolerance of the transgenic Arabidopsis was also tested (Figure 4). When the two-week-old seedlings were exposed to heat (42 °C) and recovered under normal temperature (22 °C) (Figure 4C), the survival rate of the seedlings in the OE lines was higher than that of the WT (Figure 4A,B). The OE lines had a more than 90% survival rate, whereas WT was only about 44%. These results indicate that heterologous overexpression of HuTZF3 in Arabidopsis could improve its salt and heat tolerance.

2.4. Heterologous Expression of HuTZF3 Repressed Burst of Oxidative Stress in Arabidopsis

To analyze the accumulation of ROS in WT and the HuTZF3 overexpression lines, under salt and heat stress, the leaves were stained with DAB and NBT, to detect the production of H2O2 and O2−. The results showed that the content of H2O2 and O2− in the WT accumulated more than in the HuTZF3 overexpression lines (Figure 5A,B); however, there was no significant difference between the transgenic lines and WT plants in the absence of stresses (Figure 5A,B). The activities of CAT and POD in the HuTZF3 OE lines were higher than in the WT, under salt and heat stress (Figure 5C). These results demonstrate that overexpression of HuTZF3 can improve the ROS scavenging ability of Arabidopsis, to reduce oxidative stress under salt and heat treatments.

2.5. HuTZF3 Is Co-Localized with PBs and SGs Markers in Arabidopsis

Since most TZFs are RNA-binding proteins involved in RNA regulation, and localized to PBs and SGs, the mRNA degradation factor DCP2 has decapping activity and is involved in PBs assembly, and the RNA-binding protein UBP1B, is required for SG formation. Therefore, DCP2 and UBP1B are known as PB marker and SG marker, respectively [25]. To explore whether HuTZF3 is localized to PBs and SGs, subcellular localization of HuTZF3 was performed. Protoplasts isolated from Arabidopsis leaves were co-transformed with HuTZF3-GFP and PBs marker RFP-DCP2 or SGs marker RFP-UBP1 (Figure 6). The HuTZF3-GFP was diffusely localized in the cytoplasm under the control condition. However, after heat (Figure 6A,B) and salt treatments (Figure 6C,D), HuTZF3-GFP was redistributed to cytoplasmic foci, to co-localize with the PBs and SGs markers. Although SG cytoplasmic foci were not evident under normal conditions, SG foci appeared in the cytoplasm under heat and salt stress (Figure 6B,D). These results showed that HuTZF3 is mainly localized in the cytoplasm under normal conditions and assembled into cytoplasmic foci to co-localize with PBs and SGs during the salt and heat treatment, indicating that HuTZF3 may participate in the RNA processing.

3. Discussion

The CCCH-type zinc finger proteins have been confirmed to play important roles in plant growth, development, and stress adaption. Here, we identified a total of 81 CCCH genes from pitaya, which were divided into 11 subfamilies based on the classification in Arabidopsis [21], and nine of them responded to both heat and salt stress (Figure 1 and Figure 2), indicating that the nine CCCH genes may play roles in the tolerance of pitaya to both salt and heat stress. HuTZF3 may affect RNA processing to play a role in salt and heat tolerance of pitaya, since it is localized in the PBs and SGs (Figure 6). The IX subfamily of the HuCCCH family, contained 16 HuTZFs, which are characterized by two CCCH zinc finger motifs arranged in tandem (Figure S2). Based on the presence of the Ankyrin repeat (ANK) domain, the 16 HuTZFs were further divided into two groups: RR-TZF group and ANK-RR-TZF group, which is consistent with phylogenetic analysis of the CCCH genes in Arabidopsis, rice, and maize [21,33]. Promoter cis-element analysis showed that HuTZFs are involved in plant growth and development, and respond to multiple hormones and environmental stress (Figure S1), possibly like other plants [34,35,36]. Analysis of the transcriptomic data showed that the expression of nine genes could be regulated by both salt and heat stress (Figure 2A), implying that they may play roles in pitaya’s tolerance to heat and salt stress.
Heterologous expression of HuTZF3, confirmed that some pitaya TZFs play a role in tolerance to salt and heat stress (Figure 3 and Figure 4). HuTZF3 is expressed in different organs of pitaya, with a high level in the roots and stems, and its expression in pitaya seedlings is induced by both salt and heat stress (Figure 2). This result implies that HuTZF3 may contribute to pitaya tolerance to salt and heat stress, like AtTZF1-3 [27,29] and rice OsTZF1,5,8 [30,37,38]. Salinity and heat stress induced excessive ROS production and ultimately lead to oxidative stress. DAB and DBT staining revealed more ROS accumulation in the WT Arabidopsis than the HuTZF3 OE lines under salt and heat stress (Figure 5A,B), the activities of CAT and POD in the HuTZF3 OE lines were higher than in WT Arabidopsis, under salt and heat stress (Figure 5C). These results indicate that HuTZF3 could improve tolerance to oxidative stress, to confer salt and heat stress, like rice OsTZF1 [30].
In eukaryotes, cellular mRNAs are coated with proteins forming messenger ribonucleoprotein (mRNP) complexes [39]. The mRNP complex involves post-transcriptional regulation via controlling mRNA’s whole life cycle, from pre-mRNA processing to mRNA transport, localization, stability, and translation [40]. Many inactive translation mRNAs often assemble with proteins to format cytoplasmic mRNP granules. Processing bodies (PBs) and stress granules (SGs) are two well-characterized mRNP granules, that are widely appear during various stresses [41,42]. PBs have a major involvement in mRNA decay and translation repression, SGs also contain many stalled preinitiation complexes [43]. Our results indicated that HuTZF3 can localize to PBs and SGs under salt and heat stress (Figure 6). It is known that PB- and SG-localized OsTZF1 and OsTZF7 affect RNA stability, via binding mRNA, to delay senescence and improve plant stress tolerance [30,31]. The salt and heat stress could promote accumulation of HuTZF3 in PBs and SGs (Figure 6), this suggests that HuTZF3 might also be involved in the regulation of targeting RNA metabolism in post-transcriptional and translational levels, to confer salt and heat stress in pitaya.

4. Materials and Methods

4.1. Plant and Growth Conditions

Pitaya (Hylocereus polyrhizus) and Arabidopsis were used as the plant materials in this experiment. The pitaya seeds were germinated and cultivated in the plant growth room (25 °C, 16 h/8 h light/dark photoperiod). Arabidopsis was cultivated in the plant growth room (22 °C, 16 h/8 h light/dark photoperiod).

4.2. Abiotic Stress Treatment

For pitaya stress treatment, pitaya seeds were germinated in the soil and the seedlings were grown in plates filled with nutrient soil at 25 °C, the pitaya plants were subjected to salt or heat stress. For salt on primary root growth assay, Arabidopsis seeds were germinated vertically on MS medium for 5 days, then seedlings of similar root length were chosen to transfer to MS medium containing 0, 100, 150, and 200 mM NaCl, and vertically cultured for 7 days. For Arabidopsis stress treatment, Arabidopsis seedlings were transferred and grown in nutrient soil, after germination on MS medium, for 7 days, then four-week-old plants were watered with a solution with 300 mM NaCl for salt stress, or exposed to 42 °C in an incubator for heat stress.

4.3. Sequence Analysis of HuTZF Genes

The pitaya CCCH-type zinc finger proteins were obtained from the Pitaya Genomic Database (http://www.pitayagenomic.com/index.php) (accessed on 9 August 2022) [17,44]. Further, the sequences were confirmed by SMART (https://smart.embl.de/)(accessed on 10 August 2022) NCBI conserved domain search tools (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) (accessed on 10 August 2022), and Pfam (https://pfam.xfam.org/)(accessed on 10 August 2022). The sequence of AtCCCH proteins were referred to Wang et al. [21] and downloaded from TAIR (TAIR—home page (arabidopsis.org)) (accessed on 9 August 2022). The phylogenetic tree was constructed by the neighbor-joining (NJ) method, with 1000 bootstraps, in MAGE11, then visualized and optimized by iTOL (https://itol.embl.de/)( accessed on 30 August 2022). The multiple sequence alignment of the conserved domains was analyzed by GENEDOC.

4.4. RNA Isolation and RT-qPCR Analysis

Total RNA was extracted from pitaya and Arabidopsis using the Eastep Super Total RNA Extraction Kit (Promega, Beijing, China). First-strand cDNA was synthesized using GoScriptTM Reverse Transcription Mix (Promega, Beijing, China). RT-qPCR reactions were performed with MonAmpTM ChemoHS qPCR Mix (Monad, Wuhan, China), by Roche Light Cycler 480 Real-time PCR System (Roche, Basel, Switzerland). Arabidopsis Actin2 and pitaya HuEF1-α were used as internal reference genes [45]. The primers of RT-qPCR are listed in Supplementary Table S2.

4.5. Vector Construction and Genetic Transformation

The full-length HuTZF3 cDNA was cloned into the pCAMBIA1302 vector driven by CaMV35S, to construct the HuTZF3 overexpression vector. Arabidopsis transgenic plants were produced by the Agrobacterium-mediated floral dipping method [46]. Positive transgenic plants were screened on MS medium by kanamycin and confirmed by PCR, until transgenic homozygous lines were obtained.

4.6. Histochemical and Physiological Analysis of Oxidative Stress

After the heat and salt treatment for 4 h, leaves were submerged in 1 mg/mL DAB or 1 mg/mL NBT solution within 10 h, for in situ detection of the superoxide (O2−) anion and hydrogen peroxide (H2O2), and washing in 95% ethanol [47]. Peroxidase (POD) and catalase (CAT) activities were measured using POD and CAT Assay Kits (Nanjing Jiancheng, Nanjing, China), according to the manufacturer’s instructions.

4.7. Subcellular Localization of HuTZF3

The coding sequences of HuTZF3 were inserted into the pUC/GFP vector, to construct a fusion plasmid (HuTZF3-GFP). The RFP fusion plasmids were constructed by adding the coding sequence of DCP2 and UBP1 to pBI221/RFP, which were as described in [48]. Arabidopsis mesophyll protoplasts were isolated from four-week-old Arabidopsis leaves and transformed by PEG-CaCl2-mediated transfection. After incubating the transformed protoplasts at room temperature for 12–16 h in darkness, the protoplasts were then subjected to 39 °C for heat stress, or 150 mM NaCl for salt stress. Protoplasts were observed by using confocal laser microscopy Leica SP8 STED 3X (Leica Microsystems, Mannheim, Germany).

5. Conclusions

To comprehensively examine the CCCH gene family in pitaya, a genome-wide investigation identified 81 HuCCCHs, which were classified into 11 subfamilies. Analysis of the transcriptomic data found that 9 HuCCCHs, including HuTZF3, responded to both salt and heat stress. HuTZF3 is constitutively expressed in different organs of pitaya, with a high level in the roots and stems. RT-qPCR confirmed that expression of HuTZF3 is induced by both salt and heat stress. Overexpression of HuTZF3 improved Arabidopsis tolerance to salt and heat stress. Co-localization of HuTZF3 with PBs and SGs was observed under salt and heat stress. Our findings suggest that HuTZF3 may participate in RNA metabolism to cope with the salt and heat stress of pitaya.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/ijms24076359/s1.

Author Contributions

M.Z. and W.X. designed and wrote the manuscript. S.J. provided some pitaya materials and performed some experiments. W.X. and K.X. performed most of the experiments. J.L. performed some experiments. Y.W. conducted some information analysis. K.X. and M.Z. conceived the project. All authors have read and agreed to the published version of the manuscript.

Funding

This work was funded by the Guangdong Science and Technology Program (2019B21201005), the National Key Research & Development Program of China (2022YFC3103700), and the Science and Technology Project of Zhanjiang, Guangdong, China (2021A05030).

Data Availability Statement

The data that support the findings of this study are available in the supplementary material of this article.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Tubiello, F.N.; Soussana, J.F.; Howden, S.M. Crop and pasture response to climate change. Proc. Natl. Acad. Sci. USA 2007, 104, 19686–19690. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  2. Yamaguchi, T.; Blumwald, E. Developing salt-tolerant crop plants: Challenges and opportunities. Trends Plant Sci. 2005, 10, 615–620. [Google Scholar] [CrossRef] [PubMed]
  3. Zhang, H.; Zhou, J.F.; Kan, Y.; Shan, J.X.; Ye, W.W.; Dong, N.Q.; Guo, T.; Xiang, Y.H.; Yang, Y.B.; Li, Y.C.; et al. A genetic module at one locus in rice protects chloroplasts to enhance thermotolerance. Science 2022, 376, 1293–1300. [Google Scholar] [CrossRef]
  4. Zhuang, Y.L.; Zhang, Y.F.; Sun, L.P. Characteristics of fibre-rich powder and antioxidant activity of pitaya (Hylocereus undatus) peels. Int. J. Food Sci. Technol. 2012, 47, 1279–1285. [Google Scholar] [CrossRef]
  5. Nong, Q.D.; Zhang, M.Y.; Chen, J.T.; Zhang, M.; Cheng, H.P.; Jian, S.G.; Lu, H.F.; Xia, K.F. RNA-Seq de novo assembly of red pitaya (Hylocereus polyrhizus) roots and differential transcriptome analysis in response to salt stress. Trop. Plant Biol. 2019, 12, 55–66. [Google Scholar] [CrossRef]
  6. Jiao, Z.L.; Xu, W.J.; Nong, Q.D.; Zhang, M.; Jian, S.G.; Lu, H.F.; Chen, J.T.; Zhang, M.Y.; Xia, K.F. An integrative transcriptomic and metabolomic analysis of red pitaya (Hylocereus polyrhizus) seedlings in response to heat stress. Genes 2021, 12, 1714. [Google Scholar] [CrossRef] [PubMed]
  7. Raveh, E.; Gersani, M.; Nobel, P.S. CO2 uptake and fluorescence responses for a shade-tolerant cactus Hylocereus undatus under current and doubled CO2 concentrations. Physiol. Plant 1995, 93, 505–511. [Google Scholar] [CrossRef]
  8. Garcia, T.M.; Heyduk, K.; Kuzmick, E.; Mayer, J.A. Crassulacean acid metabolism biology. New Phytol. 2014, 204, 738–740. [Google Scholar] [CrossRef] [PubMed]
  9. Males, J.; Griffiths, H. Stomatal biology of CAM plants. Plant Physiol. 2017, 174, 550–560. [Google Scholar] [CrossRef] [Green Version]
  10. Winter, K.; Smith, J.A.C. CAM photosynthesis: The acid test. New Phytol. 2022, 233, 599–609. [Google Scholar] [CrossRef]
  11. Luttge, U. Ability of crassulacean acid metabolism plants to overcome interacting stresses in tropical environments. AoB Plants 2010, 2010, plq005. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  12. Fan, Q.J.; Yan, F.X.; Qiao, G.; Zhang, B.X.; Wen, X.P. Identification of differentially-expressed genes potentially implicated in drought response in pitaya (Hylocereus undatus) by suppression subtractive hybridization and cDNA microarray analysis. Gene 2014, 533, 322–331. [Google Scholar] [CrossRef] [PubMed]
  13. Zhou, J.L.; Wang, Z.; Mao, Y.Y.; Wang, L.J.; Xiao, T.J.; Hu, Y.; Zhang, Y.; Ma, Y.H. Proteogenomic analysis of pitaya reveals cold stress-related molecular signature. PeerJ 2020, 8, e8540. [Google Scholar] [CrossRef] [Green Version]
  14. Nie, Q.; Gao, G.L.; Fan, Q.J.; Qiao, G.; Wen, X.P.; Liu, T.; Peng, Z.J.; Cai, Y.Q. Isolation and characterization of a catalase gene “HuCAT3” from pitaya (Hylocereus undatus) and its expression under abiotic stress. Gene 2015, 563, 63–71. [Google Scholar] [CrossRef]
  15. Qu, Y.J.; Nong, Q.D.; Jian, S.G.; Lu, H.F.; Zhang, M.Y.; Xia, K.F. An AP2/ERF gene, HuERF1, from pitaya (Hylocereus undatus) positively regulates salt tolerance. Int. J. Mol. Sci. 2020, 21, 4586. [Google Scholar] [CrossRef] [PubMed]
  16. Li, A.L.; Wen, Z.; Yang, K.; Wen, X.P. Conserved miR396b-GRF regulation is involved in abiotic stress responses in pitaya (Hylocereus polyrhizus). Int. J. Mol. Sci. 2019, 20, 2501. [Google Scholar] [CrossRef] [Green Version]
  17. Chen, J.Y.; Xie, F.F.; Cui, Y.Z.; Chen, C.B.; Lu, W.J.; Hu, X.D.; Hua, Q.Z.; Zhao, J.; Wu, Z.J.; Gao, D.; et al. A chromosome-scale genome sequence of pitaya (Hylocereus undatus) provides novel insights into the genome evolution and regulation of betalain biosynthesis. Hort. Res. 2021, 8, 164. [Google Scholar] [CrossRef]
  18. Takatsuji, H. Zinc-finger transcription factors in plants. Cell. Mol. Life Sci. 1998, 54, 582–596. [Google Scholar] [CrossRef]
  19. Moore, M.; Ullman, C. Recent developments in the engineering of zinc finger proteins. Brief. Funct. Genomic Proteomic 2003, 1, 342–355. [Google Scholar] [CrossRef] [Green Version]
  20. Berg, J.M.; Shi, Y.G. The galvanization of biology: A growing appreciation for the roles of zinc. Science 1996, 271, 1081–1085. [Google Scholar] [CrossRef]
  21. Wang, D.; Guo, Y.H.; Wu, C.G.; Yang, G.D.; Li, Y.Y.; Zheng, C.C. Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice. BMC Genom. 2008, 9, 44. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  22. Bogamuwa, S.P.; Jang, J.C. Tandem CCCH zinc finger proteins in plant growth, development and stress response. Plant Cell Physiol. 2014, 55, 1367–1375. [Google Scholar] [CrossRef] [PubMed]
  23. Becerra, C.; Jahrmann, T.; Puigdomènech, P.; Vicient, C.M. Ankyrin repeat-containing proteins in Arabidopsis: Characterization of a novel and abundant group of genes coding ankyrin-transmembrane proteins. Gene 2004, 340, 111–121. [Google Scholar] [CrossRef]
  24. Qu, J.; Kang, S.G.; Wang, W.; Musier-Forsyth, K.; Jang, J.C. Arabidopsis thaliana tandem zinc finger 1 (AtTZF1) protein in RNA binding and decay. Plant J. 2014, 78, 452–467. [Google Scholar] [CrossRef] [Green Version]
  25. Ivanov, P.; Kedersha, N.; Anderson, P. Stress granules and processing bodies in translational control. Cold Spring Harb. Perspect. Biol. 2019, 11, a032813. [Google Scholar] [CrossRef]
  26. Decker, C.J.; Parker, R. P-bodies and stress granules: Possible roles in the control of translation and mRNA degradation. Cold Spring Harb. Perspect. Biol. 2012, 4, a012286. [Google Scholar] [CrossRef] [Green Version]
  27. Lin, P.C.; Pomeranz, M.C.; Jikumaru, Y.; Kang, S.G.; Hah, C.; Fujioka, S.; Kamiya, Y.; Jang, J.C. The Arabidopsis tandem zinc finger protein AtTZF1 affects ABA- and GA-mediated growth, stress and gene expression responses. Plant J. 2011, 65, 253–268. [Google Scholar] [CrossRef]
  28. Pomeranz, M.C.; Hah, C.; Lin, P.C.; Kang, S.G.; Finer, J.J.; Blackshear, P.J.; Jang, J.C. The Arabidopsis tandem zinc finger protein AtTZF1 traffics between the nucleus and cytoplasmic foci and binds both DNA and RNA. Plant Physiol. 2010, 152, 151–165. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  29. Lee, S.J.; Jung, H.J.; Kang, H.S.; Kim, S.Y. Arabidopsis zinc finger proteins AtC3H49/AtTZF3 and AtC3H20/AtTZF2 are involved in ABA and JA responses. Plant Cell Physiol. 2012, 53, 673–686. [Google Scholar] [CrossRef]
  30. Jan, A.; Maruyama, K.; Todaka, D.; Kidokoro, S.; Abo, M.; Yoshimura, E.; Shinozaki, K.; Nakashima, K.; Yamaguchi-Shinozaki, K. OsTZF1, a CCCH-tandem zinc finger protein, confers delayed senescence and stress tolerance in rice by regulating stress-related genes. Plant Physiol. 2013, 161, 1202–1216. [Google Scholar] [CrossRef] [Green Version]
  31. Guo, C.M.; Chen, L.L.; Cui, Y.C.; Tang, M.; Guo, Y.; Yi, Y.; Li, Y.; Liu, L.Q.; Chen, L. RNA binding protein OsTZF7 traffics between the nucleus and processing podies/stress granules and positively regulates drought stress in rice. Front. Plant Sci. 2022, 13, 802337. [Google Scholar] [CrossRef]
  32. Chen, C.J.; Chen, H.; Zhang, Y.; Thomas, H.R.; Frank, M.H.; He, Y.H.; Xia, R. TBtools: An integrative toolkit developed for interactive analyses of big biological data. Mol. Plant 2020, 13, 1194–1202. [Google Scholar] [CrossRef] [PubMed]
  33. Peng, X.J.; Zhao, Y.; Cao, J.G.; Zhang, W.; Jiang, H.Y.; Li, X.Y.; Ma, Q.; Zhu, S.W.; Cheng, B.J. CCCH-type zinc finger family in maize: Genome-wide identification, classification and expression profiling under abscisic acid and drought treatments. PLoS ONE 2012, 7, e40120. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  34. Guo, Y.H.; Yu, Y.P.; Wang, D.; Wu, C.A.; Yang, G.D.; Huang, J.G.; Zheng, C.C. GhZFP1, a novel CCCH-type zinc finger protein from cotton, enhances salt stress tolerance and fungal disease resistance in transgenic tobacco by interacting with GZIRD21A and GZIPR5. New Phytol. 2009, 183, 62–75. [Google Scholar] [CrossRef]
  35. Chai, G.H.; Hu, R.B.; Zhang, D.Y.; Qi, G.; Zuo, R.; Cao, Y.P.; Chen, P.; Kong, Y.Z.; Zhou, G.K. Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa). BMC Genom. 2012, 13, 253. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  36. Hu, X.; Zuo, J.F. The CCCH zinc finger family of soybean (Glycine max L.): Genome-wide identification, expression, domestication, GWAS and haplotype analysis. BMC Genom. 2021, 22, 511. [Google Scholar] [CrossRef]
  37. Selvaraj, M.G.; Jan, A.; Ishizaki, T.; Valencia, M.; Dedicova, B.; Maruyama, K.; Ogata, T.; Todaka, D.; Yamaguchi-Shinozaki, K.; Nakashima, K.; et al. Expression of the CCCH-tandem zinc finger protein gene OsTZF5 under a stress-inducible promoter mitigates the effect of drought stress on rice grain yield under field conditions. Plant Biotechnol. J. 2020, 18, 1711–1721. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  38. Seong, S.Y.; Shim, J.S.; Bang, S.W.; Kim, J.K. Overexpression of OsC3H10, a CCCH-zinc finger, improves drought tolerance in rice by regulating stress-related genes. Plants 2020, 9, 1298. [Google Scholar] [CrossRef]
  39. Erickson, S.L.; Lykke-Andersen, J. Cytoplasmic mRNP granules at a glance. J. Cell. Sci. 2011, 124, 293–297. [Google Scholar] [CrossRef] [Green Version]
  40. Buchan, J.R. mRNP granules. assembly, function, and connections with disease. RNA Biol. 2014, 11, 1019–1030. [Google Scholar] [CrossRef] [Green Version]
  41. Anderson, P.; Kedersha, N. RNA granules: Post-transcriptional and epigenetic modulators of gene expression. Nat. Rev. Mol. Cell Biol. 2009, 10, 430–436. [Google Scholar] [CrossRef] [PubMed]
  42. Maruri-Lopez, I.; Figueroa, N.E.; Hernandez-Sanchez, I.E.; Chodasiewicz, M. Plant stress granules: Trends and beyond. Front. Plant Sci. 2021, 12, 722643. [Google Scholar] [CrossRef]
  43. Guzikowski, A.R.; Chen, Y.S.; Zid, B.M. Stress-induced mRNP granules: Form and function of processing bodies and stress granules. Wiley Interdiscip. Rev. RNA 2019, 10, e1524. [Google Scholar] [CrossRef] [PubMed]
  44. Chen, C.B.; Li, F.P.; Xie, F.F.; Chen, J.X.; Hua, Q.Z.; Chen, J.Y.; Wu, Z.J.; Zhang, Z.K.; Zhang, R.; Zhao, J.T.; et al. Pitaya genome and multiomics database (PGMD): A comprehensive and integrative resource of Selenicereus undatus. Genes 2022, 13, 745. [Google Scholar] [CrossRef]
  45. Nong, Q.D.; Yang, Y.C.; Zhang, M.Y.; Zhang, M.; Chen, J.T.; Jian, S.G.; Lu, H.F.; Xia, K.F. RNA-seq-based selection of reference genes for RT-qPCR analysis of pitaya. FEBS Open Bio 2019, 9, 1403–1412. [Google Scholar] [CrossRef] [Green Version]
  46. Clough, S.J.; Bent, A.F. Floral dip: A simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 1998, 16, 735–743. [Google Scholar] [CrossRef] [Green Version]
  47. Kumar, D.; Yusuf, M.A.; Singh, P.; Sardar, M.; Sarin, N.B. Histochemical detection of superoxide and H2O2 accumulation in Brassica juncea seedlings. Bio-Protocol 2014, 4, e1108. [Google Scholar] [CrossRef]
  48. Gutierrez-Beltran, E.; Moschou, P.N.; Smertenko, A.P.; Bozhkov, P.V. Tudor staphylococcal nuclease links formation of stress granules and processing bodies with mRNA catabolism in Arabidopsis. Plant Cell 2015, 27, 926–943. [Google Scholar] [CrossRef] [Green Version]
Ijms 24 06359 g001 550
Figure 1. Systematic identification of the CCCH-type zinc finger protein genes from pitaya. (A) Chromosomal locations of pitaya CCCH genes. The chromosomal locations of HuCCCH genes were mapped by TBtools [32]. Names of the HuCCCH genes are shown on the right of the chromosomes. The scale of the genome size is shown on the left. (B) Phylogenetic tree of the CCCH proteins from pitaya and Arabidopsis. The 81 HuCCCH proteins from pitaya and the 68 AtCCCH proteins from Arabidopsis were used to construct the phylogenetic tree by MAG11 and visualized by iTOL. The red star indicates HuTZF3.
Figure 1. Systematic identification of the CCCH-type zinc finger protein genes from pitaya. (A) Chromosomal locations of pitaya CCCH genes. The chromosomal locations of HuCCCH genes were mapped by TBtools [32]. Names of the HuCCCH genes are shown on the right of the chromosomes. The scale of the genome size is shown on the left. (B) Phylogenetic tree of the CCCH proteins from pitaya and Arabidopsis. The 81 HuCCCH proteins from pitaya and the 68 AtCCCH proteins from Arabidopsis were used to construct the phylogenetic tree by MAG11 and visualized by iTOL. The red star indicates HuTZF3.
Ijms 24 06359 g001
Ijms 24 06359 g002 550
Figure 2. Expression response of pitaya CCCH genes to salt and heat stress. (A,B) Heatmap of HuCCCHs response to heat (A) and salt (B) stress. The transcriptomic data cited are from Nong et al. (2019) [5] and Jiao et al. (2021) [6]. The three-month-old seedlings grown in a greenhouse, were treated with 450 mM NaCl, or at 42 °C, for different times, then the samples were collected for RNA-seq. (C–E) Expression pattern of HuTZF3 in different tissues of pitaya (C), and in pitaya seedlings under salt (D) and heat (E) treatment. Three-month-old pitaya seedlings were treated with 450 mM NaCl (D) at 42 °C (E). HuEF1-α was used as the internal reference gene. Values represent means ± SD (n = 3 technical repetitions). All RT-qPCR analyses for gene expression were performed in three biological replicates, with similar results.
Figure 2. Expression response of pitaya CCCH genes to salt and heat stress. (A,B) Heatmap of HuCCCHs response to heat (A) and salt (B) stress. The transcriptomic data cited are from Nong et al. (2019) [5] and Jiao et al. (2021) [6]. The three-month-old seedlings grown in a greenhouse, were treated with 450 mM NaCl, or at 42 °C, for different times, then the samples were collected for RNA-seq. (C–E) Expression pattern of HuTZF3 in different tissues of pitaya (C), and in pitaya seedlings under salt (D) and heat (E) treatment. Three-month-old pitaya seedlings were treated with 450 mM NaCl (D) at 42 °C (E). HuEF1-α was used as the internal reference gene. Values represent means ± SD (n = 3 technical repetitions). All RT-qPCR analyses for gene expression were performed in three biological replicates, with similar results.
Ijms 24 06359 g002
Ijms 24 06359 g003 550
Figure 3. Heterologous expression of HuTZF3 improved salt tolerance in Arabidopsis. (A,B) Phenotype of seedlings’ root growth (A) and statistical analysis of primary root length (B) on MS medium with NaCl. Five-day-old Arabidopsis seedlings were transferred to MS medium, containing 0, 100, 150, and 200 mM NaCl and cultured for 7 days. The scale bar is 1 cm. (C) The expression level of HuTZF3 in the wild type (WT) and overexpressed HuTZF3 transgenic Arabidopsis lines. AtActin2 was used as the internal reference gene. (D,E) Four-week-old Arabidopsis of WT and overexpressing HuTZF3 lines were subjected to 300 mM NaCl treatment (D), and their survival rate (E). The scale bar is 1 cm. The experiments were performed three times with similar results. Values are means ± SD (n = 30 plants). Asterisks show the values that are significant compared to WT. * p < 0.05, ** p < 0.01 according to the Student’s t-test.
Figure 3. Heterologous expression of HuTZF3 improved salt tolerance in Arabidopsis. (A,B) Phenotype of seedlings’ root growth (A) and statistical analysis of primary root length (B) on MS medium with NaCl. Five-day-old Arabidopsis seedlings were transferred to MS medium, containing 0, 100, 150, and 200 mM NaCl and cultured for 7 days. The scale bar is 1 cm. (C) The expression level of HuTZF3 in the wild type (WT) and overexpressed HuTZF3 transgenic Arabidopsis lines. AtActin2 was used as the internal reference gene. (D,E) Four-week-old Arabidopsis of WT and overexpressing HuTZF3 lines were subjected to 300 mM NaCl treatment (D), and their survival rate (E). The scale bar is 1 cm. The experiments were performed three times with similar results. Values are means ± SD (n = 30 plants). Asterisks show the values that are significant compared to WT. * p < 0.05, ** p < 0.01 according to the Student’s t-test.
Ijms 24 06359 g003
Ijms 24 06359 g004 550
Figure 4. Heterologous expression of HuTZF3 enhanced tolerance to heat stress in Arabidopsis. (A,B) Two-week-old Arabidopsis WT and overexpressing HuTZF3 plants were exposed to heat treatment (A), and their survival rate (B) after recovering. The experiments were repeated three times with similar results. Values are means ± SD (n = 40 plants). Asterisks show the values that are significant compared to WT. * p < 0.05 according to the Student’s t-test. The scale bar is 1 cm. (C) Schematic diagram of heat treatment conditions.
Figure 4. Heterologous expression of HuTZF3 enhanced tolerance to heat stress in Arabidopsis. (A,B) Two-week-old Arabidopsis WT and overexpressing HuTZF3 plants were exposed to heat treatment (A), and their survival rate (B) after recovering. The experiments were repeated three times with similar results. Values are means ± SD (n = 40 plants). Asterisks show the values that are significant compared to WT. * p < 0.05 according to the Student’s t-test. The scale bar is 1 cm. (C) Schematic diagram of heat treatment conditions.
Ijms 24 06359 g004
Ijms 24 06359 g005 550
Figure 5. Oxidative stress analysis of the transgenic Arabidopsis with HuTZF3 overexpression. (A,B) Detection of H2O2 and O2− by DAB (A) and NBT (B) staining. (C) The activity of CAT and POD under salt and heat treatments. Four-week-old Arabidopsis WT and overexpression HuTZF3 plants were exposed to 300 mM NaCl for 4 h, and 42 °C for 4 h. Three replicates of the experiments were performed. Values are means ± SD (n = 3). Asterisks show the values that are significant compared to WT. ** p < 0.01 according to the Student’s t-test.
Figure 5. Oxidative stress analysis of the transgenic Arabidopsis with HuTZF3 overexpression. (A,B) Detection of H2O2 and O2− by DAB (A) and NBT (B) staining. (C) The activity of CAT and POD under salt and heat treatments. Four-week-old Arabidopsis WT and overexpression HuTZF3 plants were exposed to 300 mM NaCl for 4 h, and 42 °C for 4 h. Three replicates of the experiments were performed. Values are means ± SD (n = 3). Asterisks show the values that are significant compared to WT. ** p < 0.01 according to the Student’s t-test.
Ijms 24 06359 g005
Ijms 24 06359 g006 550
Figure 6. HuTZF3 co-localized with RNA processing bodies (PBs) and stress granules (SGs) marker proteins under heat and salt stress. (A,B) The HuTZF3-GFP was co-transformed with the PB marker RFP-DCP2 (A) and the SG marker RFP-UBP1 (B) into Arabidopsis protoplasts, and then cultured under control conditions (22 °C), or heat stress, at 39 °C for 30 min, before observation. (C,D) The HuTZF3-GFP was co-transformed with the PB marker RFP-DCP2 (C) and the SG marker RFP-UBP1 (D) into Arabidopsis protoplasts, and then cultured under control conditions, or salt stress with 150 mM NaCl for 1 h, before observation. Scale bar = 10 μm.
Figure 6. HuTZF3 co-localized with RNA processing bodies (PBs) and stress granules (SGs) marker proteins under heat and salt stress. (A,B) The HuTZF3-GFP was co-transformed with the PB marker RFP-DCP2 (A) and the SG marker RFP-UBP1 (B) into Arabidopsis protoplasts, and then cultured under control conditions (22 °C), or heat stress, at 39 °C for 30 min, before observation. (C,D) The HuTZF3-GFP was co-transformed with the PB marker RFP-DCP2 (C) and the SG marker RFP-UBP1 (D) into Arabidopsis protoplasts, and then cultured under control conditions, or salt stress with 150 mM NaCl for 1 h, before observation. Scale bar = 10 μm.
Ijms 24 06359 g006
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Xu, W.; Jian, S.; Li, J.; Wang, Y.; Zhang, M.; Xia, K. Genomic Identification of CCCH-Type Zinc Finger Protein Genes Reveals the Role of HuTZF3 in Tolerance of Heat and Salt Stress of Pitaya (Hylocereus polyrhizus). Int. J. Mol. Sci. 2023, 24, 6359. https://doi.org/10.3390/ijms24076359

AMA Style

Xu W, Jian S, Li J, Wang Y, Zhang M, Xia K. Genomic Identification of CCCH-Type Zinc Finger Protein Genes Reveals the Role of HuTZF3 in Tolerance of Heat and Salt Stress of Pitaya (Hylocereus polyrhizus). International Journal of Molecular Sciences. 2023; 24(7):6359. https://doi.org/10.3390/ijms24076359

Chicago/Turabian Style

Xu, Weijuan, Shuguang Jian, Jianyi Li, Yusang Wang, Mingyong Zhang, and Kuaifei Xia. 2023. "Genomic Identification of CCCH-Type Zinc Finger Protein Genes Reveals the Role of HuTZF3 in Tolerance of Heat and Salt Stress of Pitaya (Hylocereus polyrhizus)" International Journal of Molecular Sciences 24, no. 7: 6359. https://doi.org/10.3390/ijms24076359

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop