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Genome-wide characterization of the CPA gene family in potato and a preliminary functional analysis of its role in NaCl tolerance

BMC Genomics volume 25, Article number: 144 (2024) Cite this article

Abstract

Background

The cation/proton antiporter (CPA) superfamily plays a crucial role in regulating ion homeostasis and pH in plant cells, contributing to stress resistance. However, in potato (Solanum tuberosum L.), systematic identification and analysis of CPA genes are lacking.

Results

A total of 33 StCPA members were identified and classified into StNHX (n = 7), StKEA (n = 6), and StCHX (n = 20) subfamilies. StCHX owned the highest number of conserved motifs, followed by StKEA and StNHX. The StNHX and StKEA subfamilies owned more exons than StCHX. NaCl stress induced the differentially expression of 19 genes in roots or leaves, among which StCHX14 and StCHX16 were specifically induced in leaves, while StCHX2 and StCHX19 were specifically expressed in the roots. A total of 11 strongly responded genes were further verified by qPCR. Six CPA family members, StNHX1, StNHX2, StNHX3, StNHX5, StNHX6 and StCHX19, were proved to transport Na+ through yeast complementation experiments.

Conclusions

This study provides comprehensive insights into StCPAs and their response to NaCl stress, facilitating further functional characterization.

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Background

Salt stress severely impacts plant growth and yield, affecting over 800 million hectares of land globally and hindering sustainable agriculture [1, 2]. NaCl, the most soluble and widely distributed soil salt, is absorbed by roots, accumulating in tissues and resulting in damage to plants [1, 3]. Throughout evolution, plants developed various mechanisms to regulate the intracellular ion balance and resist salt stress, relying on ion transporters in cell and organelle membranes [4].

The cation-proton antiporters (CPA) superfamily is a vital class of proteins in plants, facilitating the transport of Na+ as well as cations, such as K+ and Li+ [5,6,7]. The CPA superfamily comprises two broad categories, named CPA1 and CPA2 [8]. CPA1 includes the Na+/H+ exchanger family (NHX) [9, 10], while CPA2 includes the K+ efflux antiporter (KEA) and cation/H+ exchanger (CHX) family [5, 9]. CPA identification has been reported in various plants like Arabidopsis thaliana [11, 12], rice (Oryza sativa L.) [13], grape (Vitis vinifera L.) [14], wheat (Triticum aestivum L.) [15], radish (Raphanus sativus L.) [16], and tomato (Solanum lycopersicum L.) [17]. The AtCPAs reside in the plasma membrane, vacuoles, and chloroplasts, enabling ion exchange and transport, especially for monovalent cations in plants, including sodium and potassium ions [18, 19]. The CPA superfamily maintains cytoplasmic ion homeostasis and enhances salt tolerance through Na+ efflux and regionalization. NHX proteins have been reported in over 60 plant species [20]. The Arabidopsis NHX family comprises eight members (AtNHX1-AtNHX8) [21,22,23] involved in Na+ and H+ exchange and transport. AtNHX1 was the first characterized NHX gene, significantly enhancing salt tolerance in transgenic yeast or plants [21, 24]. Overexpressing AtNHX7 reduced Na+ accumulation in the xylem and stem, improving salt tolerance in transgenic A. thaliana [11]. The NHX1 gene was reported to regulate salt tolerance in Arachis hypogaea and Helianthus tuberosus [25, 26]. Cloned from a drought-hardy legume, VuNHX1 can also regulate salt tolerance [27]. In rice, OsNHX1-5 and OsNHX7/OsSOS1 have been identified to enhance salt tolerance [28, 29]. OsCHX14 played a role in the K+ homeostasis process [30]. AtKEA1-AtKEA3 played crucial roles in chloroplast osmoregulation and pH homeostasis [18], while AtKEA2 regulated K+ and pH in plastids [31]. The CHX family proteins were involved in K+, Na+, and H+ transport. A total of 28 CHX genes were identified in A. thaliana [32]. AtCHX13, AtCHX17, AtCHX20, and AtCHX23 predominantly transported K+ rather than Na+ [9]. AtCHX14, AtCHX21, AtCHX23, and AtCHX24 played roles in K+ redistribution, salt tolerance, chloroplast development, pH homeostasis, and leaf senescence [33,34,35,36].

Potato (Solanum tuberosum L.) is the world’s third-largest food crop, valued for its rich nutrition, high yield, and adaptability. However, potato is relatively sensitive to salt stress. Excess salt in the soil reduces photosynthetic rates, disrupts ion balance, and impairs osmotic regulation, affecting tuber growth and development, leading to yield loss. Identifying genes conferring resistance to abiotic stress is crucial for molecular breeding in potato. Although some CPA genes have been linked to NaCl stress response in other plants, detailed information on CPA in potatoes remains limited. Our study aimed to systematically identify the CPA superfamily in the potato genome and analyze their phylogenetic relationship, gene structure, and conserved motifs. Additionally, we investigated the expression patterns of StCPAs under salt (NaCl) treatment and confirmed the sodium ion transport function of StNHX1, StNHX2, StNHX3, StNHX5, StNHX6 and StCHX19. These findings lay the groundwork for further understanding of the role of StCPAs in NaCl stress responses.

Results

Identification and characterization of CPAs in potato

To identify CPA members in potato, we performed a BLAST search against the potato protein database using known CPA sequences from Arabidopsis. We identified 33 StCPA members in the potato genome, categorized into three subfamilies: StNHXs (n = 7), StCHXs (n = 20), and StKEAs (n = 6). The genes were named StNHX1-StNHX7, StCHX1-StCHX20, and StKEA1-StKEA6 based on homologies with other species. Detailed information, such as gene name, coding region length, protein length, molecular weight, theoretical isoelectric point (pI), and subcellular localization predictions for all members, were analyzed (Table 1). Notably, all StCPAs contained a Na+/H+ exchange domain, with lengths of 281 to 1,828 amino acid and molecular weights of 30 to 206 kDa. The theoretical pI ranged from 4.48 to 9.76, indicating different protein charges. The subcellular localization of StCPA predicted by WoLF PSORT, and most of them were on the plasma membrane, in line with the function of maintaining Na+ homeostasis as transporters. In addition, StCPA are located on several organelles, including the endoplasmic reticulum, vacuole, cytoplasm, golgi apparatus and peroxisome.

Table 1 Physiochemical properties of StCPA genes
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Phylogenetic tree and chromosome localization analysis

To analyze the phylogenetic relationships of all StCPAs members, we extracted full-length CPA protein sequences from potato, Arabidopsis, tomato, radish and grape, then aligned them to construct the neighbor-joining (NJ) phylogenetic tree (Fig. 1).

Fig. 1
figure 1

Phylogenetic tree of CPA proteins in potato, Arabidopsis, tomato, radish and grape. Neighbor-joining tree constructed using MEGA 11, depicting the phylogenetic relationship among 174 CPA proteins, comprising 40 AtCPAs, 33 StCPAs, 26 SlCPAs, 48 RsCPAs and 27 VvCPAs. The NHX, KEA, and CHX subfamilies encompass 23 members, 28 members, and 123 members, respectively

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In total, 174 CPA proteins from five species (33 from potato, 40 from Arabidopsis, 26 from tomato, 48 from radish and 27 from grape) were categorized into three subfamilies: NHX, KEA, and CHX. Among them, the NHX group has 23 members, and the KEA group has 28 members. The CHX group is the most abundant subfamily, with 123 members, including 19, 22, 35, 27 and 20 from tomato, grape, radishe, Arabidopsis and potatoe, respectively. The phylogenetic tree indicated that the CPA gene family was highly conserved in different species.

The StCPAs were mapped on the 12 chromosomes, and they unevenly distributed across different chromosomes, with one to seven genes on each chromosome (Fig. 2). Chromosome 8 had the most CPA members (seven), followed by five on chromosome 6 and four on chromosome 1. Chromosomes 4 and 5 each had three members, while chromosomes 2, 3, 9, and 12 each had two members. The remaining chromosomes each contained one member.

Fig. 2
figure 2

Chromosomal position of StCPA genes. Distribution of StCPA genes in potato chromosomes. Chromosome numbers are shown within each bar. The scale on the left is in megabases (Mb)

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Conserved motifs and gene structure analysis

To distinguish the differences among the three StCPA families, we conducted an analysis of the gene composition and structure of the StCPA proteins (Fig. 3). StCHX members exhibited three to eleven conserved motifs, while KEA members had four to five conserved motifs. In the StNHXs family, StNHX3 and StNHX6 had no conserved motifs, StNHX1 and StNHX2 had only one conserved motif, StNHX4, and StNHX5 had two conserved motifs, and StNHX7 had four conserved motifs (Fig. 3A). Notably, most StCPA members within the same subfamily had similar motif compositions, implying conserved functions among these proteins. Additionally, the number of motifs varied across different subfamilies, with CHXs being the most abundant, followed by KEAs and NHXs (Fig. 3B). This suggests that the functions of different subfamilies may have evolved different functions over time.

Fig. 3
figure 3

Conserved motifs of StCPA proteins. A Analysis of the conserved domains of the StCPA proteins. The 10 motifs are depicted using different color ranges. B Number of conserved motifs in StNHX, StKEA, and StCHX subfamilies

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We further analyzed the structural diversity of these StCPA (Fig. 4). The results revealed significant variations in sequence length and the number of introns/exons among StCPA members. The CHX family members had shorter sequence lengths and fewer exons, whereas the NHX and KEA family members had longer sequence lengths with many shorter exons (Fig. 4A and B). For instance, the StKEA6 gene spans 46,476 bp and consists of 19 exons, while the StCHX6 gene spans 2,596 bp and contains only 3 exons. This pattern is consistent with the CPA gene superfamily of tomato [17].

Fig. 4
figure 4

Structural analysis of the StCPA gene superfamily. A Structures of StCPA gene superfamily. Introns and exons are represented as thin lines and green boxes, respectively. B Number of exons in StNHX, StKEA, and StCHX subfamilies

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RNA-seq analysis of the CPA gene superfamily under NaCl stress

To investigate the potential function of the StCPA superfamily under NaCl stress, we analyzed their expression patterns in leaves and roots under 200 mM NaCl treatment using RNA-seq data. The results revealed that the expression levels of 19 StCPAs were enhanced in roots or leaves under NaCl treatment (Fig. 5A). Notably, StCHX14 and StCHX16 exhibited specific high expression in leaves, while StCHX2 and StCHX19 are specifically expressed in roots, indicating that they may be specifically involved in regulating ion homeostasis in leaves or roots, thereby affecting NaCl tolerance (Fig. 5A and B). Interestingly, the remaining members (n = 14) of StCHX were not induced by NaCl stress, indicating that they may transport other cations but Na+. In contrast, all StNHX and StKEA were induced by NaCl stress, highlighting their potential roles in potato NaCl stress. Collectively, our findings suggest that StCPA members are differentially induced by NaCl stress and play distinct roles in NaCl resistance.

Fig. 5
figure 5

Expression of StCPA genes under NaCl treatment. A Heatmap of CPA superfamily RNA-Seq under NaCl stress. B Specific expression of genes StCHX14 and StCHX16 in leaves. C Specific expression of genes StCHX2 and StCHX19 in roots. Potatoes were subjected to 200 mM NaCl for 0 h, 6 h, 12 h, 24 h, and 48 h. Root samples (R0, R6, R12, R24, R48) and leaf samples (L0, L6, L12, L24, L48) were collected for RNA-Seq analysis. The asterisk indicates a significant difference (*p < 0.05)

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Quantitative expression analysis of StCPAs under NaCl stress

The expression of this family was further validated by qPCR analysis under NaCl stress (Fig. 6). We selected 11 StCPA genes (StNHX1, StNHX2, StNHX3, StNHX4, StNHX5, StNHX6, StNHX7, StCHX19, StKEA1, StKEA2, and StKEA4) that exhibited substantial induction by NaCl stress (Delta FPKM relative to CK > 10 in root or leaf). In roots, the expression level of StNHX4 induced by NaCl stress is the highest (> 6-fold at the 24th hour). StNHX3, StNHX6, StNHX7, StCHX19, and StKEA1 were induced to 2–3 folds. StNHX1, StNHX2, StNHX5, and StKEA2 were significantly upregulated (p < 0.05), while the change of StKEA4 was not significant. Notably, most of genes showed gradually increased expression with the prolongation of stress treatment, except for StNHX6 with the highest upregulation at the12th hour. In leaves, the expression levels of StNHX3 and StNHX7 were quickly upregulated at the 6th hours (> 2-fold and > 1.5-fold) and remained this level; StNHX1, StNHX5, StNHX6, StCHX19, and StKEA4 showed a trend of upregulation and then downregulation. Among them, StNHX1, StNHX5, StNHX6, and StCHX19 showed the highest upregulation at the 12th hour and downregulation at the 24th hour, while StKEA4 showed the highest upregulation at the 6th hours and gradually downregulated thereafter. The expression level of StNHX2 was steadily upregulated in the leaves, while the other genes StNHX4, StKEA1, and StKEA2 were not induced by NaCl stress in the leaves. In addition, we noticed that the induced expression levels of StNHX3, StNHX4, StCHX19, StKEA1, and StKEA2 were higher in the roots than in the leaves, while the induced expression levels of StNHX1, StNHX5, StNHX6, and StKEA4 in the leaves were higher in the roots. In summary, different StCPA members exhibited various responsive patterns, indicating their diverse functions in response to NaCl stress.

Fig. 6
figure 6

Quantitative RT-PCR expression analysis of the CPA gene superfamily. Expression profiles (qPCR) of the StCPA genes at different time intervals (0 h, 3 h, 6 h, 12 h, and 24 h) under 200 mM NaCl treatments. The relative expression levels at different stress treatment times were compared to the control (0 h). The asterisk indicates a significant difference (*p < 0.05;**p < 0.01); ns indicates the difference is not significant based on the t-test (p ≥ 0.05)

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Effect of NaCl stress on yeast cell growth

In order to verify whether these responsive genes own the Na+ transport function, we selected seven genes, which strongly responded to NaCl stress both in roots and leaves, for validation using defective yeast expression experiments. These genes included StNHX1, StNHX2, StNHX3, StNHX5, StNHX6, StNHX7, and StCHX19. Under normal conditions, the growth of untransformed and transgenic strains is similar. Under NaCl stress, untransformed yeast cells AXT3K-P416 cannot grow on AP-URA medium, while the transgenic strains containing the functional genes could grow on AP-URA medium. The yeast strain that AXT3K + p416-StNHX7 present the phenotype similar to AXT3K + P416 and cannot grow on AP-URA medium containing 60 mM NaCl, indicating that StNHX7 does not have Na+ transport function. It is speculated that this gene is responsible for transporting cations other than Na+. In contrast, AXT3K strains transformed StNHX1, StNHX2, StNHX3, StNHX5, StNHX6, and StCHX19 genes could grow in 60 mM NaCl AP-URA medium, indicating that these genes have Na+ transport functions. StNHX5 and StNHX6 showed the comparable phenotype with the positive control (W303 + P416), indicating their effective functions. The other members growth status was not as strong as the positive control W303 + P416, indicating that they only partially rescued the Na+ deficient phenotype of the AXT3K strain (Fig. 7). These results are consistent with previous research [15, 37].

Fig. 7
figure 7

Effect of NaCl stress on yeast cell growth. The wild-type strain (W303 + P416), mutant cells (AXT3K + P416), and recombinant strains (AXT3K + P416-StNHX1, AXT3K + P416-StNHX2, AXT3K + P416-StNHX3, AXT3K + P416-StNHX5, AXT3K + P416-StNHX6, AXT3K + P416-StNHX7, and AXT3K + P416-StCHX19) were grown to saturation, and then 10-µL serial decimal dilutions were spotted onto AP-URA plates supplemented with 0 and 60 mM NaCl. Exogenous uracil was provided by the P416 vector to ensure normal growth of the strain in the AP-URA medium

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Discussion

In this study, we identified 33 CPA members in potato, classified into three subfamilies: CHX, NHX, and KEA. This classification was consistent with previous research on various plant species, including monocotyledons and dicotyledons like rice, maize, sorghum, A. thaliana, grape, and tomato [5, 11,12,13,14,15,16,17], This indicates that the evolution and classification of CPA proteins in different species is highly conserved. This study will provide reference for the subsequent functional characterization of the potato CPA gene family (Fig. 1). We observed significant differences in the number of conserved motifs among the subfamilies, with 0–4 motifs for StNHX, 4–5 motifs for StKEA, and 3–11 motifs for StCHX. Similar observations have been found in other species. For instance, in tomato, the number of motifs for SlNHX, SlKEA, and SlCHX is 0–2, 4–7, and 7–13, respectively [17]. In wheat, the number of motifs for TaNHX, TaKEA, and TaCHX is 1–4, 7–9, and 3–11, respectively [15]. In radish, the number of motifs for RsNHX, RsKEAs, and RsCHX is 1–4, 4–5, and 3–17, respectively [16]. Moreover, we also observed common features in the number of exons in different subfamilies across various species. For StNHXs, StKEAs, and StCHXs, the numbers of exons are 14–33, 19–20, and 2–9, respectively. Similarly, in tomato, the numbers are 1–23, 7–20, and 2–7 [17]. In wheat, the numbers are 7–25, 12–21, and 1–4 [15]. In radish, the numbers are 10–19, 17–21, and 1–5, respectively [16]. This consistency among different species indicates that CPAs are relatively conserved during evolution.

To date, numerous studies have reported the involvement of the CPA gene superfamily in NaCl tolerance in plants [9, 38]. Our qPCR results demonstrated that all 11 selected StCPA genes were upregulated in response to NaCl stress in leaves or roots, indicating that upregulating the expression of antiporters is an important mechanism for coping with NaCl stress. SOS1 (Salt overly sensitive 1) protein, a Na+/H+ antiporter found in various plants, is induced by NaCl stress and functions in Na+ efflux to enhance NaCl tolerance in plants [1, 3, 39]. In potato, StNHX1 is the homologous gene of AtSOS1. We observed significant induction of StNHX1 by NaCl stress in both leaves and roots of potato, consistent with our expectations. Furthermore, we noticed tissue-specific differences in gene expression. RNA-Seq showed that StCHX14 and StCHX16 were specifically expressed in leaves, while StCHX2 and StCHX19 were specifically expressed in roots. qPCR data showed that the expression level of StNHX4 increased by 7 folds in the roots after 24 h of NaCl stress, while it was not significant in the leaves. This further proved that StNHX4 play the major role in the roots. StKEA4 showed a significant increase in expression levels, but not induced in the roots, suggesting that this gene mainly plays a role in the leaves. So, it is speculated that different members have different tissues-specific functional divergence of regulating NaCl tolerance.

In addition, we observed that the expression levels of all StNHX and most (5/6) StKEA members significantly increased in roots or leaves under NaCl stress. For StCHX subfamily, six members (StCHX9, StCHX15, StCHX2, StCHX19, StCHX14, and StCHX16) induced by NaCl stress, while most of (n = 14) members were not sensitive to NaCl stress. This indicated StNHX and StKEA play major roles in coping with NaCl stress, while StCHX subfamily members may be induced by various forms of salt stress.

The yeast system for rapid verification of CPA function has been widely employed in various plants [15, 40, 41]. For instance, heterologous expression of ZmNHX5, ZmCHX2, ZmCHX3, ZmCHX5, ZmCHX17, and ZmKEA2 restored the Na+ resistance of the yeast mutant AXT3K, and the NaCl tolerance function of ZmCHX2 and ZmNHX5 was confirmed in transgenic plants [40]. Similarly, the wheat CPA gene superfamily TaNHX4 enhanced the survival rate of Escherichia coli under various abiotic stresses [15]. In Arabidopsis, the AtKEA subfamily, except for AtKEA3, improved the tolerance of yeast mutant strains to high K+ stress [41]. To verified which member own ion transport function, a total of seven genes were applied to a yeast system. The results showed that heterologous expression of StNHX1, StNHX2, StNHX3, StNHX5, StNHX6, and StCHX19 enhanced the NaCl tolerance of AXT3K, indicating that these genes indeed have potential Na+ efflux function. However, StNHX7 did not rescue the defective expression of AXT3K, indicating that it does not have Na+ efflux function. It is speculated that this gene is induced to respond to NaCl stress and affects potato NaCl tolerance by transporting other metal ions.

Conclusions

In this study, we conducted a comprehensive investigation of the CPA superfamily members in potato. A total of 33 StCPA genes were identified and categorized into three subfamilies: NHX, KEA, and CHX, with significant differences in conserved motifs and exons. More than half of the StCPA genes were induced by NaCl stress, exhibiting varying magnitudes and response times. Notably, StNHX1, StNHX2, StNHX3, StNHX5, StNHX6, and StCHX19 were found to transport Na+ and enhance NaCl tolerance in defective yeast mutants. These findings provide valuable insights for future research on the biological functions and molecular mechanisms of these potato CPA genes in response to NaCl stress.

Materials and methods

Identification of the CPA gene superfamily in potato

The Arabidopsis CPA protein sequences were acquired from the TAIR database (https://www.arabidopsis.org/index.jsp) [42]; tomato CPA protein sequences were acquired from the phytozome database (https://phytozome-next.jgi.doe.gov/) [17]; radish CPA protein sequences were acquired from the National Genomics Data Center (NGDC) Genome Sequence Archive (GSA) (https://ngdc.cncb.ac.cn/gsa/) [43]; grape CPA protein sequences were acquired from the Genome Warehouse (GWH) database of the National Genomics Data Center (https://bigd.big.ac.cn/) (Supplementary Table S3) [44]. The potato genome and amino acid sequences were obtained from the National Genome Science Data Center (https://ngdc.cncb.ac.cn/) [45], BioProject: accession no. PRJCA011810. A BLAST-P search was conducted to query the StCPA proteins within the potato protein database, and the filtering threshold was established as an E-value less than e−5. These were further verified by interrogating the Pfam database (http://pfam.xfam.org/search/) [46] for the existence of a signature Na+/H+ exchanger (PF00999) domain. A total of 33 StCPA gene superfamily proteins were identified for subsequent analysis. Additionally, ExPASy ProtParam (https://www.expasy.org/) was employed to predict the physicochemical properties of StCPA proteins, including the length of the coding region, number of amino acids, molecular weight, theoretical isoelectric point (pI) [47]. Subcellular location of the StCPAs proteins predicted by WoLF PSORT (https://www.genscript.com/wolf-psort.html/) [40].

Phylogenetic tree and chromosome localization analysis

Use MEGA11 software to align the CPA protein sequences of potato, Arabidopsis, tomato, radish, and grape, to construct a neighbor-joining (NJ) phylogenetic tree. The chromosomal positions of different StCPA genes were identified based on the National Genomics Data Center (https://ngdc.cncb.ac.cn/) [45], BioProject: accession no. PRJCA011810. The chromosomal map was visualized using the Ritchie-lab phenogram tool (http://visualization.ritchielab.org/phenograms/plot/).

Conserved motifs and gene structure analysis

The potato StCPA gene superfamily sequence information was consistent with the above method. The structural information related to the StCPA genes was displayed using TBtools (https://github.com/CJ-Chen/TBtools/) [48]. The conserved motifs were identified by Multiple Em for Motif Elicitation (MEME) (http://meme.nbcr.net/meme/tools/meme/) [49].

Planting and CPA gene superfamily RNA-Seq analysis

The potato genotype A056 was propagated using MS medium and cultured for 15 days in a growth room (conditions: light duration of 16 h, dark duration of 8 h; temperature of 21 ℃) and transplanted into a matrix block (the matrix block material is composed of coconut bran, peat, and wood, and after high-temperature sterilization, it was wrapped in a degradable mesh like non-woven fabric to form 41 mm × 42 mm sized matrix block). The seedlings were cultured for 2–3 days and grown normally over the course of 15 days. Add NaCl into tap water and prepare 200 mM NaCl aqueous solution and pour it into a seedling tray for potato seedlings to absorb and form NaCl stress. Leaf and root samples were collected from seedlings at 0 h, 6 h, 12 h, 24 h, and 48 h after NaCl treatment and flash-frozen in liquid nitrogen. Three biological replicates for each treatment were conducted. RNA was extracted using the TRIzol reagent method, and StCPA transcriptome analysis was performed. RNA-Seq was completed by the Beijing Annuo Company, China. The FPKM expression value was determined from the sequencing data and were further screened by heatmap drawing using TBtools software.

Quantitative real-time PCR

The RNA samples for qPCR were identical to those used for RNA-Seq analysis. The first strand cDNA synthesis from total RNA reverse transcription was performed using the PrimeScriptâ„¢ RT reagent Kit with gDNA Eraser (Perfect Real Time) from TaKaRa. Quantitative RT-PCR was performed using TB Green Premix Ex Taq II (Tli RNaseH Plus) (Code No. RR820A/B) from TaKaRa on a StepOnePlus Real-Time PCR Instrument (Applied Biosystems). Tubulin was employed as an internal control to normalize the samples. Primer design was conducted using Primer Premier 5 software and is outlined in Supplementary Table S1. All experiments were conducted with biological triplicates.

Cloning of gene

Plant material accession A056 was utilized for total RNA extraction and reverse transcription polymerase chain reaction to generate cDNA sequences (an identical method to the described qPCR procedure). Primers were designed based on the CDS of StNHX1, StNHX2, StNHX3, StNHX5, StNHX6, StNHX7, and StCHX19 from potato DM genomes. Detailed primer sequences can be found in Supplementary Table S2. In order to clone the coding region sequences of the StNHX1, StNHX2, StNHX3, StNHX5, StNHX6, StNHX7, and StCHX19 genes, the cDNA of the A056 material was employed as a template for PCR amplification using the Supplementary Table S2 primers. The sequences of the StNHX1, StNHX2, StNHX3, StNHX5, StNHX6, StNHX7, and StCHX19 genes were amplified and inserted into the P416 vector using the seamless cloning method (In-Fusion® Snap Assembly Master Mix) (TaKaRa). Finally, vector construction was verified by sequencing. The constructed vectors included P416-StNHX1, P416-StNHX2, P416-StNHX3, P416-StNHX5, P416-StNHX6, P416-StNHX7, and P416-StCHX19.

Yeast strains and incubation

Saccharomyces cerevisiae strain AXT3K (â–³ena1::HIS3::â–³ena4,â–³nha1::LEU2, and â–³nhx1:: KanMX4), deficient in the main endogenous Na+ transporters, was used and is a derivative of W303 (MAT ura3-1 leu2-3,112 his3-11,15 trp1-1 ade2-1 can1-100) [37, 50]. To assess the functionality of the StNHX1, StNHX2, StNHX3, StNHX5, StNHX6, StNHX7, and StCHX19 proteins, p416-StNHX1, p416-StNHX2, p416-StNHX3, p416-StNHX5, p416-StNHX6, p416-StNHX7, and p416-StCHX19 were transformed into AXT3K. Additionally, an empty P416 vector was transformed into W303 as a positive control and AXT3K as a negative control. The transformed strains were grown using an AP-URA medium for 72 h (AP culture medium comes from Shanghai Huzhen limited company, the instructions for use are detailed in the user manual). When precultures grew to saturation, they were diluted 100-fold, 1,000-fold, and 10,000-fold. Samples consisting of 2 µL of each series of diluents were dotted onto AP-URA plates containing 0 mM NaCl and 60 mM NaCl. After incubation for 3–5 days at 30 Â°C, growth was visualized and analyzed.

Availability of data and materials

The datasets generated and/or analyzed during the current study are available in the National Center for Biotechnology Information repository, (https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/sra/PRJNA1016159, accession number - PRJNA1016159).

References

  1. Yang Y, Guo Y. Elucidating the molecular mechanisms mediating plant salt-stress responses. New Phytol. 2018;217:523–39.

    Article  CAS  PubMed  Google Scholar 

  2. Munns R, Tester M. Mechanisms of salinity tolerance. Ann Rev Plant Biol. 2008;59:651–81.

    Article  CAS  Google Scholar 

  3. Yang Y, Guo Y. Unraveling salt stress signaling in plants. J Integr Plant Biol. 2018;60(9):796–804.

    Article  CAS  PubMed  Google Scholar 

  4. Gong Z, Xiong L, Shi H, Yang S, Herrera L, Xu G, et al. Plant abiotic stress response and nutrient use efficiency. Sci China Life Sci. 2020;63:635–74.

    Article  PubMed  ADS  Google Scholar 

  5. Ye CY, Yang X, Xia X, Yin WL. Comparative analysis of cation/proton antiporter superfamily in plants. Gene. 2013;521:245–51.

    Article  CAS  PubMed  Google Scholar 

  6. Brett CL, Donowitz M, Rao R. Evolutionary origins of eukaryotic sodium/proton exchangers. Am J Physiol-Cell Ph. 2005;288:C223-239.

    Article  CAS  Google Scholar 

  7. Evans AR, Hall D, Pritchard J, Newbury HJ. Retracted: The roles of the cation transporters CHX21 and CHX23 in the development of Arabidopsis thaliana. J Ex Bot. 2012;63:59–67.

    Article  CAS  Google Scholar 

  8. Pires IS, Negrao S, Pentony MM, Abreu IA, Oliveira MM, Purugganan MD. Different evolutionary histories of two cation/proton exchanger gene families in plants. BMC Plant Biol. 2013;13:1–12.

    Article  Google Scholar 

  9. Chanroj S, Wang G, Venema K, Zhang MW, Delwiche CF, Sze H. Conserved and diversified gene families of monovalent cation/H+ antiporters from algae to flowering plants. Front Plant Sci. 2012;3:25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Jia Q, Zheng C, Sun S, Amjad H, Liang K, Lin W. The role of plant cation/proton antiporter gene family in salt tolerance. Biol Plant. 2018;62:617–29.

    Article  CAS  Google Scholar 

  11. Qiu QS, Guo Y, Dietrich MA, Zhu JK. Regulation of SOS1, a plasma membrane Na+/H+ exchanger in Arabidopsis thaliana, by SOS2 and SOS3. P Natl A Sci USA. 2002;99:8436–41.

    Article  CAS  ADS  Google Scholar 

  12. Cellier F, Conejero G, Ricaud L, Luu DT, Lepetit M, Gosti F, et al. Characterization of AtCHX17, a member of the cation/H+ exchangers, CHX family, from Arabidopsis thaliana suggests a role in K+ homeostasis. Plant J. 2004;39:834–46.

    Article  CAS  PubMed  Google Scholar 

  13. Zeng Y, Li Q, Wang H, Zhang JL, Du J, Feng HM, et al. Two NHX-type transporters from Helianthus tuberosus improve the tolerance of rice to salinity and nutrient deficiency stress. Plant Biotechnol J. 2018;16:310–21.

    Article  CAS  PubMed  Google Scholar 

  14. Ma Y, Wang J, Zhong Y, Cramer GR, Cheng ZM. Genome-wide analysis of the cation/proton antiporter (CPA) super family genes in grapevine (Vitis vinifera L.). Plant Omics. 2015;8:300–11.

  15. Sharma H, Taneja M, Upadhyay SK. Identification, characterization and expression profiling of cation-proton antiporter superfamily in Triticum aestivum L. and functional analysis of TaNHX4-B. Genomics. 2020;112:356–70.

    Article  CAS  PubMed  Google Scholar 

  16. Wang Y, Ying J, Zhang Y, Xu L, Zhang WT, Ni M, et al. Genome-wide identification and functional characterization of the cation proton antiporter (CPA) family related to salt stress response in radish (Raphanus sativus L). Int J Mol Sci. 2020;21:8262.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Hussain Z, Khan H, Imran M, Naeem MK, Shah SH, Iqbal A, et al. Cation/Proton antiporter genes in tomato: genomic characterization, expression profiling, and co-localization with salt stress-related QTLs. Agronomy. 2022;12:245.

    Article  CAS  Google Scholar 

  18. Kunz HH, Gierth M, Herdean A, Cruz MS, Kramer DM, Spetea C, et al. Plastidial transporters KEA1, 2, and-3 are essential for chloroplast osmoregulation, integrity, and pH regulation in Arabidopsis. P Natl A Sci USA. 2014;111:7480–5.

    Article  CAS  ADS  Google Scholar 

  19. Han L, Li JL, Wang L, Shi WM, Su YH. Identification and localized expression of putative K+/H+ antiporter genes in Arabidopsis. Acta Physiol Plant. 2015;37:1–14.

    Article  Google Scholar 

  20. Pardo JM, Cubero B, Leidi EO, Quintero FJ. Alkali cation exchangers: roles in cellular homeostasis and stress tolerance. J Exp Bot. 2006;57:1181–99.

    Article  CAS  PubMed  Google Scholar 

  21. Apse MP, Aharon GS, Snedden WA, Blumwald E. Salt tolerance conferred by overexpression of a vacuolar Na+/H+ antiport in Arabidopsis. Science. 1999;285:1256–8.

    Article  CAS  PubMed  Google Scholar 

  22. Apse MP, Sottosanto JB, Blumwald E. Vacuolar cation/H+ exchange, ion homeostasis, and leaf development are altered in a T-DNA insertional mutant of AtNHX1, the Arabidopsis vacuolar Na+/H+ antiporter. Plant J. 2003;36:229–39.

    Article  CAS  PubMed  Google Scholar 

  23. Yokoi S, Quintero FJ, Cubero B, Ruiz MT, Bressan RA, Hasegawa PM, et al. Differential expression and function of Arabidopsis thaliana NHX Na+/H+ antiporters in the salt stress response. Plant J. 2002;30:529–39.

    Article  CAS  PubMed  Google Scholar 

  24. Gaxiola RA, Rao R, Sherman A, Grisafi P, Alper SL, Fink GR. The Arabidopsis thaliana proton transporters, AtNhx1 and Avp1, can function in cation detoxification in yeast. P Natl A Sci USA. 1999;96:1480–5.

    Article  CAS  ADS  Google Scholar 

  25. Zhang WW, Meng JJ, Xing JY, Yang S, Guo F, Li XG, Wan SB. The K+/H+ antiporter AhNHX1 improved tobacco tolerance to NaCl stress by enhancing K+ retention. J Plant Biol. 2017;60:259–67.

    Article  CAS  Google Scholar 

  26. Zeng Y, Li Q, Wang HY, Zhang JL, Du J, Feng HM, Blumwald E, Yu L, Xu GH. Two NHX-type transporters from Helianthus tuberosus improve the tolerance of rice to salinity and nutrient deficiency stress. Plant Biotechnol J. 2017;16:310–21.

    Article  PubMed  PubMed Central  Google Scholar 

  27. Mishra S, Alavilli H, Lee B, Panda SK, Sahoo L. Cloning and characterization of a novel vacuolar Na+/H+ antiporter gene (VuNHX1) from drought hardy legume, cowpea for salt tolerance. Plant Cell Tissue Organ. 2015;120:19–33.

    Article  CAS  Google Scholar 

  28. Fukuda A, Nakamura A, Hara N, Toki S, Tanaka Y. Molecular and functional analyses of rice NHX-type Na+/H+ antiporter genes. Planta. 2011;233:175–88.

    Article  CAS  PubMed  Google Scholar 

  29. Sellamuthu G, Jegadeeson V, Sajeevan RS, Rajakani R, Parthasarathy P, Raju K, et al. Distinct evolutionary origins of intron retention splicing events in NHX1 antiporter transcripts relate to sequence specific distinctions in Oryza species. Front Plant Sci. 2020;11:267.

    Article  PubMed  PubMed Central  Google Scholar 

  30. Huanca-Mamani W, Ortiz MV, Cardenas-Ninasivincha S, Acosta-Garcia G, Bastias E. Gene expression analysis in response to combined salt and boron (B) stresses in a tolerant maize landrace. Plant Omics. 2018;11:80–8.

    Article  CAS  Google Scholar 

  31. Aranda-Sicilia MN, Cagnac O, Chanroj S, Sze H, Rosales MPR, Venema K. Arabidopsis KEA2, a homolog of bacterial KefC, encodes a K+/H+ antiporter with a chloroplast transit peptide. Biochim et Biophys acta (BBA)-biomembranes. 2012;818:2362–71.

    Article  Google Scholar 

  32. Sze H, Padmanaban S, Cellier F, Honys D, Cheng NH, Bock KW, et al. Expression patterns of a novel AtCHX gene family highlight potential roles in osmotic adjustment and K+ homeostasis in pollen development. Plant Physiol. 2004;136:2532–47.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Song CP, Guo Y, Qiu Q, Lambert G, Galbraith DW, Jagendorf A, et al. A probable Na+ (K+)/H+ exchanger on the chloroplast envelope functions in pH homeostasis and chloroplast development in Arabidopsis thaliana. P Natl A Sci USA. 2004;101:10211–6.

    Article  CAS  ADS  Google Scholar 

  34. Hall D, Evans AR, Newbury HJ, Pritchard J. Functional analysis of CHX21: a putative sodium transporter in Arabidopsis. J Exp Bot. 2006;57:1201–10.

    Article  CAS  PubMed  Google Scholar 

  35. Hur Y, Kim JH, Lee DJ, Chung KM, Woo HR. Overexpression of AtCHX24, a member of the cation/H+ exchangers, accelerates leaf senescence in Arabidopsis thaliana. Plant Sci. 2012;183:175–82.

    Article  CAS  PubMed  Google Scholar 

  36. Zhao J, Li P, Motes CM, Park S, Hirschi KD. CHX14 is a plasma membrane K-efflux transporter that regulates K+ redistribution in Arabidopsis thaliana. Plant Cell & Environ. 2015;38:2223–38.

    Article  CAS  Google Scholar 

  37. Zhou Y, Yin X, Duan R, Hao GP, Guo JC, Jiang XY. SpAHA1 and SpSOS1 coordinate in transgenic yeast to improve salt tolerance. PLoS ONE. 2015;10:e0137447.

    Article  PubMed  PubMed Central  Google Scholar 

  38. Padmanaban S, Chanroj S, Kwak JM, Li XY, Ward JM, Sze H. Participation of endomembrane cation/H+ exchanger AtCHX20 in osmoregulation of guard cells. Plant Physiol. 2007;144:82–93.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Shi H, Ishitani M, Kim C, Zhu JK. The Arabidopsis thaliana salt tolerance gene SOS1 encodes a putative Na+/H+ antiporter. P Natl A Sci USA. 2000;97:6896–901.

    Article  CAS  ADS  Google Scholar 

  40. Kong M, Luo M, Li J, Feng Z, Zhang Y, Song W, et al. Genome-wide identification, characterization, and expression analysis of the monovalent cation-proton antiporter superfamily in maize, and functional analysis of its role in salt tolerance. Genomics. 2021;113:1940–51.

    Article  CAS  PubMed  Google Scholar 

  41. Zheng S, Pan T, Fan L, Qiu Q. A novel AtKEA gene family, homolog of bacterial K+/H+ antiporters, plays potential roles in K+ homeostasis and osmotic adjustment in Arabidopsis. PLoS One. 2013;8:e81463.

    Article  PubMed  PubMed Central  ADS  Google Scholar 

  42. Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, et al. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 2012;40:D1202-1210.

    Article  CAS  PubMed  Google Scholar 

  43. Xu L, Wang Y, Dong JH, Zhang W, Tang MJ, Zhang WL, et al. A chromosome-level genome assembly of radish (Raphanus sativus L.) reveals insights into genome adaptation and differential bolting regulation. Plant Biotechnol J. 2023;21:990–1004.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Shi XY, Cao S, Wang X, Huang SY, Wang Y, Liu Z, et al. The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding. Hortic Res. 2023;10:uhad061.

    Article  PubMed  PubMed Central  Google Scholar 

  45. Yang X, Zhang L, Guo X, Xu JF, Zhang K, Yang YQ, et al. The gap-free potato genome assembly reveals large tandem gene clusters of agronomical importance in highly repeated genomic regions. Mol Plant. 2023;16:314–7.

    Article  CAS  PubMed  Google Scholar 

  46. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42:D222-230.

    Article  CAS  PubMed  Google Scholar 

  47. Gasteiger E, Gattiker A, Hoogland C, Lvan L, Appel RD, Bairoch A. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids R. 2003;31:3784–8.

    Article  CAS  Google Scholar 

  48. Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He YH, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020;13:1194–202.

    Article  CAS  PubMed  Google Scholar 

  49. Bailey TL. MEME-ChIP: Motif analysis of large DNA datasets. Bioinformatics. 2011;27:1696–7.

    Article  PubMed  PubMed Central  Google Scholar 

  50. Quintero FJ, Ohta M, Shi H, Pardo JM. Reconstitution in yeast of the Arabidopsis SOS signaling pathway for Na+ homeostasis. P Natl A Sci USA. 2002;99:9061–6.

    Article  CAS  ADS  Google Scholar 

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Acknowledgements

We thank Prof. Yi Wang (China Agricultural University) for kindly sharing the yeast mutant AXT3K and Prof. Zhen Wang (Anhui Agricultural University) for providing the yeast expression vector p416.

Funding

This work was supported by the National Natural Science Foundation of China (U2002204), the Breeding Program of Shandong Province, China (2022LZGC017), the Yunnan Fundamental Research Project (202001AV070003), and the Guangdong Major Project of Basic and Applied Basic Research (2021B0301030004).

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Author notes

  1. Jintao Liu and Dianjue Li contributed equally to this work.

Authors and Affiliations

  1. Key Lab for Potato Biology in Universities of Yunnan, School of Life Sciences, Yunnan Normal University, Kunming, 650500, China

    Jintao Liu, Dianjue Li, Jing Wang, Qian Wang, Qi Fu & Guangtao Zhu

  2. Southwest United Graduate School, Kunming, 650500, China

    Jintao Liu & Guangtao Zhu

  3. Institute of Vegetables, Shandong Academy of Agricultural Sciences/Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Sub-Center, Jinan, 250100, China

    Xiao Guo & Xiaohui Yang

  4. International Potato Center (CIP), CIP China Center for Asia Pacific, Beijing, 100081, China

    Philip Kear

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  1. Jintao Liu
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Contributions

G.Z., X.Y. and P.K. designed the experiments and revised the manuscript. J.L., D.L. and Q.F. analyzed the data. Q.W. and X.G. carried out partial experiments. J.L. carried out most the experiments and wrote the manuscript. All authors confirmed their contributions and approved the final manuscript.

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Correspondence to Guangtao Zhu or Xiaohui Yang.

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Supplementary Information

Additional file 1: Supplementary Table S1.

Primer sequences for qRT-PCR. Supplementary Table S2. Gene cloning primer. Supplementary Table S3. Arabidopsis, tomato, radish and grape CPA gene family information.

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Liu, J., Li, D., Wang, J. et al. Genome-wide characterization of the CPA gene family in potato and a preliminary functional analysis of its role in NaCl tolerance. BMC Genomics 25, 144 (2024). https://0-doi-org.brum.beds.ac.uk/10.1186/s12864-024-10000-2

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Keywords

BMC Genomics

ISSN: 1471-2164

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