Characters and structures of the nucleobase–ascorbate transporters (NAT) family genes in Gossypium hirsutum and their roles in responding to salt and drought stresses

Abstract

Background

Nucleobase–ascorbate transporters (NAT), synonymously called nucleobase–cation symporter 2 (NCS2) proteins, were earlier reported to be involved in plant growth, development and resistance to stress. Previous studies concluded that s a polymorphic SNP associated with NAT12 was significant different between salt-tolerant and salt-sensitive materials of upland cotton. In current study, a comprehensive analysis of NAT family genes was conducted for the first time in cotton.

Results

In this study, we discovered 32, 32, 18, and 16 NAT genes in Gossypium hirsutum, G. barbadense, G. raimondii and G. arboreum, respectively, which were classified into four groups (groups I–IV) based on the multiple sequence analysis. These GhNAT genes were unevenly distributed on At and Dt sub-genome in G. hirsutum. Most GhNAT members in the same group had similar gene structure characteristics and motif composition. The collinearity analysis revealed segmental duplication as well as tandem duplication contributing to the expansion of the GhNATs. The analysis of cis-acting regulatory elements of GhNATs showed that the function of GhNAT genes in cotton might be related to plant hormone and stress response. Under different conditions, the expression levels further suggested the GhNAT family genes were associated with plant response to various abiotic stresses. GhNAT12 was detected in the plasma membrane. And it was validated that the GhNAT12 gene played an important role in regulating cotton resistance to salt and drought stress through the virus-induced gene silencing (VIGS) analysis.

Conclusions

A comprehensive analysis of NAT gene family was performed in cotton, including phylogenetic analysis, chromosomal location, collinearity analysis, motifs, gene structure and so on. Our results will further broaden the insight into the evolution and potential functions of NAT genes in cotton. Current findings could make significant contribution towards screening more candidate genes related to biotic and abiotic resistance for the improvement in cotton.

Background

Cotton is an important economic crop around the world, due to its most common consumption as the raw material in textile industry. The genus Gossypium contains two cultivated tetraploids of G. hirsutum and G. barbadense, which originated from the transoceanic hybridization of the A-genome-like progenitor G. arboreum with the native D-genome-like ancestor G. raimondii in New World, followed by the chromosome doubling (Li et al. 2015). Subsequently, the nascent dicotyledonous allotetraploid cotton diverged into five Gossypium species. And G. hirsutum and G. barbadense independently evolved in diverse geographic regions (Hu et al. 2019). With the rise of global warming, extreme weather conditions such as rainstorm, flood, drought, typhoon, heat wave, cold wave, and sandstorm occur frequently. In addition, the excessive development and utilization of land resources led to scarcity of water and soil salinization, which have brought huge losses to agricultural production. Though, cotton is a drought and saline-alkali tolerant crop. But extreme stresse condition will cause huge losses to cotton production. So that, it is of great significance for the development of cotton industry to study the mechanism of cotton salt and drought tolerance, necessitating to mine the related functional genes, and pyramid such genetic factors in new developing varieties.

Abiotic stress responses are important mechanisms of sessile organisms such as plants which cannot survive unless capable to cope with environmental changes (Hirayama and Shinozaki 2010). The abiotic stresses mostly refer to extreme environmental conditions, are always the great threats to plant growth and yield (Grattan and Grieve 1998). Under salt stress conditions, physiological and metabolic activities are affected by ionic and osmotic stresses, nutritional imbalances, or a combination of these factors (Chen et al. 2014; Slama et al. 2015). Ionic stress mainly involves the excessive accumulation of Na⁺ in plant leaves. During periods of high salt stress, the Na⁺ uptake competes with the K⁺ uptake which results in excess of cytoplasmic Na⁺ sequestration instead of Cl⁻ within the cell (Muchate et al. 2016). This will cause osmotic imbalances, and a series of enzymatic and nonenzymatic antioxidants in plant cells, which finally lead to water deficits, stomatal closure, and reduces plant growth and the rate of photosynthesis (Jithesh et al. 2006; Gill and Tuteja 2010; Roy et al. 2014). Similarly, K⁺ as a major inorganic osmoticum gets dramatically decreased under drought stress in Malus hupehensis (Qi et al. 2019). And drought stress inhibits photosynthesis by decreasing stomatal aperture (Cornic 2000). The endomembrane trafficking is tightly linked to stress signaling pathways to meet the demand of rapid changes in cellular processes and to ensure the correct delivery of stress-related cargo molecules (Wang et al. 2020a), which had already been proved as an important regulator in osmotic stress, such as drought, salinity, and cold stresses.

Nucleobase–ascorbate transporters (NATs), also known as nucleobase–cation symporter 2 (NCS2), is a group of transporter proteins being found in almost all domains of life, which contain transporting ascorbate, pyrimidines and purines (De Koning and Diallinas 2000). The NAT family has been identified in bacteria, archaea, diatoms, fungi, plants and animals (De Koning and Diallinas 2000; Bürzle et al. 2013). The NAT family members generally have common characters, containing about 400∼650 amino acid residues and 10∼14 transmembrane domains. Within these transmembrane domains, there are two conserved domains. Of them, one is highly conserved domain located at the upstream of transmembrane segment 9 (TMS9), also called “NAT signature motif” (Q/E/P) NXGXXXXT (R/K/G) a critical domain of purine transporters UapA and UapC to recognize substrate in Aspergillus (Diallinas et al. 1998; Koukaki et al. 2005). In principle, if the first amino acid of the motif is Q/E, the protein will transport nucleic acids, or  P will transport ascorbic acid. And another highly conserved domain is a QH structure located in the middle of transmembrane segment 1 (TMS1) (Diallinas et al. 1998; Koukaki et al. 2005; Karatza et al. 2006; Gournas et al. 2008; Frillingos 2012; Kosti et al. 2012). Phylogenetic tree analysis of NAT proteins depicted five clades based on multiple sequence alignments in plant (Maurino et al. 2006; Cai et al. 2014). The NAT proteins in Arabidopsis thaliana split into five subfamilies, including I, II, III, IV and V, respectively. These classifications were closely associated with the specific expression of tissue and organ in the growth process of Arabidopsis thaliana (Maurino et al. 2006). The NAT family members are evolutionarily conserved and the nucleobase is the principal substrate of this family. Among the five known families of transporters, only the NAT family utilizes nucleobases as their principal substrate (Frillingos 2012; Kourkoulou et al. 2018). The most renowned characteristics of NAT proteins include transport uric acid, xanthine, uracil, ascorbic acid, adenine, guanine, hypoxanthine, and uracil (Gournas et al. 2008; Frillingos 2012; Bürzle et al. 2013; Niopek-Witz et al. 2014), such as AtNAT3 and AtNAT12 proteins have been proved to transport adenine, guanine, and uracil (Niopek-Witz et al. 2014). Eight Arabidopsis NATs (AtNAT1–AtNAT8) all transport xanthine (Hunt 2013).

The NAT proteins are important for plant growth and development. Some plants' NAT proteins have been functionally characterized. The maize leaf permease1 Lpe1 was the first identified NAT family member in plant. Loss of LPE1 function results in a defective chloroplast phenotype and affects the integrity of plasma membrane (Schultes et al. 1996). LPE1 acts as a transporter for xanthine and uric acid, but not for ascorbic acid (Argyrou et al. 2001). The biochemical characterization of NAT3 and NAT12 proteins from Arabidopsis thaliana have been reported to transport guanine, uracil, and adenine with high affinity (Niopek-Witz et al. 2014). The transient expression of AtNAT3 and AtNAT12 has indicated that the encoded proteins are localized in the plasma membrane (Niopek-Witz et al. 2014). Overexpression of MdNAT7 in transgenic apple plants has showed enhanced xanthine and uric acid concentrations and improved tolerance to salinity stress compared with nontransgenic plants, while opposite phenotypes have been observed in MdNAT7 RNAi plants (Sun et al. 2021).

In a previous study, SNP (Single nucleotide polymorphism) analysis has been  performed in different salt-tolerant cotton materials, and 1 282 SNPs have been screened in association with salt-tolerance (Wang et al. 2016). A nucleobase–ascorbate transporter has been identified and named as GhNAT12 (Gh_A07G117800). The SNP variation associated with NAT12 was significantly different between salt-tolerant (AA) and salt-sensitive materials (AG), which suggests that the NAT12 may be related to cotton salt-tolerance. In this study, the NATs were identified through a whole genome search in Gossypium. The gene phylogenetic relationship, gene structure, protein conserved motif, and chromosome localization were systematically analyzed in G. hirsutum. In addition, the relative expression of GhNATs under salt and drought stress was performed using qRT-PCR to validate the function of NATs. The silencing of GhNAT12 in G. hirsutum under salt and drought stress demonstrated that GhNAT12 positively regulates cotton resistance against salt and drought. Further experiments revealed that GhNAT12 is localized to the cell membrane. These results could make contribution to understand NAT family potential functions regarding resistance against abiotic stress in cotton.

Material and methods

Identification of NAT family members in cotton

Genomic sequence data and protein sequence of four cotton species G. hirsutum, G. raimondii, G. arboreum, and G. barbadense were acquired from the Cotton Functional Genomics Database (CottonFGD) (http://www.cottonfgd.org/) (Zhu et al. 2017). The Hidden Markov Mode (HMM) profile of PF00860 which most probably belongs to NAT gene family was downloaded from Pfam (https://pfam.xfam.org/). Protein sequence containing PF00860 were screened to identify the NAT candidate homologous genes containing target domain in four cotton species by HMMER software (Jones et al. 2014). Subsequently, the genes above the inclusion threshold were selected, the selected genes were stored temporarily. Using the Data Fetch & Enrichment interface on CottonFGD website, the selected genes were searched and the result in terms of the domain of PF00860 were downloaded. In order to further confirm the screened genes, the Batch Web CD-Search Tools website (https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi) was used to screen the genes associated domains. The genome sequence data of A. thaliana was retrieved from JGI Phytozome 13 (https://phytozome.jgi.doe.gov/). We obtained some features of NAT genes in cotton, as for amino acid length of the protein, isoelectric points (pI), molecular weights (MWs), grand average of hydropathy (GRAVY) and so on, by using CottonFGD (http://www.cottonfgd.org/).

Phylogentic analysis

To discover the evolutionary relationship of NAT family in different species, amino acid sequences of NATs identified in G. hirsutum, G. raimondii, G. arboreum, G. barbadense, and A. thaliana were applied to conduct multiple sequence alignment utilizing the Clustalw program (Edgar 2004). Subsequently, the phylogenetic tree was constructed using the neighbor joining (NJ) method with the Poisson substitution model by MEGA7.0 (Kumar et al. 2016).

Chromosomal locations and collinearity analysis of NAT genes in Gossypium hirsutum

The physical chromosomal location of all NAT genes in G. hirsutum were generated by TBtools software (Chen et al. 2018). Gene information was obtained from CottonFGD and CottonGen (https://www.cottongen.org/) (Yu et al. 2013). MCScanX software was used to analyze genomic collinearity blocks (Wang et al. 2012). The diagrammatical result of NAT from G. hirsutum was visualized by using Circos-0.69 software (Krzywinski et al. 2009).

Gene structure analysis and conserved motif identification

The conserved protein motifs were identified using Multiple Em for Motif Elicitation (MEME) website (http://meme-suite.org/) (Bailey et al. 2009). The MAST (Motif Alignment & Search Tool) file from the MEME website, the NWK (Newick) file from the phylogenetic tree analysis and the GFF3 (General Feature Format Version 3) genome file from G. hirsutum were used to visualize the phylogenetic tree, conservative protein motif and the gene structure map by the TBtools software.

Analysis of GhNATs promoter regions and differentially expressed genes

DNA sequences of the 2 000 bp upstream regions of GhNATs were extracted from CottonFGD database (http://www.cottonfgd.org/) as promoter regions. The PlantCARE website (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/) was used for the prediction of cis-acting elements. The RNA-seq data (PRJNA248163) was downloaded from National Center for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov/). The expression levels of NAT genes were analysized under salt, cold, hot, and PEG stress (Hu et al. 2019). And the localization of cis-acting elements were drawn using the TBtools software.

Plant materials and abiotic stresses

The upland cotton (G. hirsutum) cv. Zhong9807 is a salt tolerant cultivar, H177 is a drought tolerant cultivar (Wang et al. 2016; Lu et al. 2017). The cotton plants and Nicotiana benthamiana were sown in soil and seedlings were grown in greenhouse under 8 h (dark)/16 h (light), at 23 °C (dark)/28 °C (light) with a relative humidity of 60%.

The three-leaf stage seedlings of Zhong9807 were treated with 200 mmol·L⁻¹ NaCl, and the drought stress was carried out on H177 with 12% PEG6000 (Wang et al. 2020b). At 0, 1, 3, 6, 9, and 12 h, the leaves of cotton were collected and immediately frozen with liquid nitrogen, then stored at − 80 °C before RNA extraction.

qRT-PCR analysis

Total RNA was extracted from cotton leaves using RNA prep Pure Plant Kit (TIANGEN) according to the protocol provided by the manufacturer. First-strand cDNA was generated using Prime ScriptTM II First Strand cDNA Synthesis Kit (Takara) according to the manufacturer’s instructions. Quantitative real-time PCR (qRT-PCR) was performed following with the previously program (Zhang et al. 2021). The expression level of NAT genes was analyzed by the $2^{{-\Delta \Delta \text{C}}_t}$ method. And the cotton histone3 (GenBank accession No. AF024716) gene was used as the internal reference gene. Three independent biological and technical repeats were performed. The primers used in qRT-PCR were listed in Additional file 1: Table S1.

GhNAT12 gene silenced

The fragments (Additional file 1: Table S1) of GhNAT12 were integrated into the tobacco rattle virus vector pYL156 plasmid at the XbaI-SacI site using the T4 DNA ligase (Takara) to form the pYL156-GhNAT12 vector. And then the vector were transformed into Agrobacterium tumefaciens GV3101. The pYL156-PDS was used as a positive control, and the empty pYL156 plasmid was the negative control. Agrobacterium harboring the empty vector of pYL-156 or one of its derivatives (pYL15-GhNAT12, pYL156-PDS) were mixed with an equal volume of Agrobacterium harboring pYL192. When the cotton plants were 7 days old, each mixture was infiltrated into two fully expanded cotyledons of cotton plants until filled with the entire cotyledons as previously described (Fan et al. 2021). Seedlings were grown at 25 °C in dark treatment for 24 h, and then incubated with a 16 h (light) /8 h (dark) photoperiod. When the TRV:PDS plants displayed albino phenotype in their newly developed true leaves, the TRV:00 and TRV:GhNAT12 infiltrated Zhong9807 were treated with 200 mmol·L⁻¹ NaCl and the TRV:00 and TRV:GhNAT12 infiltrated H177 were treated with 12% PEG6000 at the same time to observe their response to salt and drought stress. The expression level of the GhNAT12 were examined, and the successfully silenced plants were used to evaluate the resistance against salt and drought stresses.

Subcellular localization

To observe the subcellular localization of GhNAT12, the open reading frame of GhNAT12 was fused to GFP (Green fluorescent protein) under the control of 35S promoter in the expression vector pCAMBIA3300 to generate pCAMBIA3300-GhNAT12-GFP constructs. And the vectors were transiently expressed in tobacco (Nicotiana benthamiana) leaf cells by A. tumefaciens strain GV3101 infiltration method. The infiltrated plants were incubated for 2∼3 d at 23 °C under dark condition. The GFP fluorescence signals were detected using confocal microscopy (Olympus FV1200). Primers used in this study were listed in Additional file 1: Table S1.

For visualization of GhNAT12 in onion epidermal cells, recombinant plasmids of pCAMBIA3300-GhNAT12-GFP were transformed into onion epidermal cells by particle bombardment using the PDS-1000/He system (Bio-Rad, USA). After incubation on MS medium for 24∼36 h, GFP fluorescence was visualized by confocal microscopy. For plasmolysis experiment, cells were treated with 20% sucrose. Signals were visualized by confocal microscopy.

Results

Phylogenetic analysis of NAT genes

To clarify the evolutionary relationship of NAT genes in cotton, we identified 32, 32, 18, and 16 NATs in G. hirsutum, G. barbadense, G. arboreum, and G. raimondii (Additional file 2: Table S2), respectively. The phylogenetic tree of cotton and A. thaliana NATs had been constructed by MEGA 7 using the neighbor-joining (NJ) method. The results showed that all NAT genes in five species were classified into four different groups (I–IV) (Fig. 1). Group I included 46 cotton NATs and AtNAT4–AtNAT10 in Arabidopsis thaliana. Group II consisted 12 cotton NATs and AtNAT11, AtNAT12. The second largest group was III, containing 25 cotton NATs and AtNAT1, AtNAT2. The group IV consisted of 15 cotton NATs and AtNAT3. From the evolutionary distance on phylogenetic tree, homelogous genes were identified. A total of 9 pairs were higher similarly and identity. Interestingly, the diploid species of G. raimondii and G. arboreum were less as compared with the tetraploids of G. hirsutum and G. barbadense. This indicated that there was a presumed gene loss event during the evolutionary process.

Fig. 1

Phylogenetic tree of the NAT family proteins in different plant species. The phylogenetic tree of NAT proteins was constructed using the Neighbor Joining method. NAT proteins were clustered into four groups

Chromosome localization of GhNATs genes

To further investigate the genomic distribution of NAT family genes, the chromosome map of 32 NAT members from G. hirsutum were constructed (Fig. 2). A total of 16 genes were located on 8 chromosomes of At sub-genome and 16 genes were positioned on 9 chromosomes of Dt sub-genome. The distribution pattern of NAT genes was uneven on the At and Dt chromosomes. The maximum number of NAT members on the same chromosome were four, and those genes were located on the D05 chromosome. The minimum number of NAT members presented on the same chromosome was one, occuring at chromosome A04, A06, A10, D03, D04, D06, D10. The distribution of some NATs in terms of number and position on the chromosome of At were the same as the chromosome of Dt, such as A04–D04, A06–D06, A10–D10, A11–D11, A12–D12. The result indicated that the genes were conserved during evolution. Comparing with the homeologous chromosome of At, Dt sub-genome, Gh_D05G262700 and Gh_A07G067200 were distinctive, it might be the result of incomplete genome assembly. Some genes were distributed on different chromosomes, which implied that these genes might been added or lost during the evolution process. There were more NAT homologues in A03, A05 than D03, D05, suggested the possible gene loss event. Based on the primitive resistance genes, the gene loss event might arise before polyploid formation during the evolution. And this statement requries further verification.

Fig. 2

Chromosomal locations of NAT genes in Gossypium hirsutum

Collinearity relationship of GhNATs genes

To identify paralogous gene pairs of At and Dt sub-genomes in G. hirsutum, the NAT genes locus on chromosome and collinearity analysis were investigated (Fig. 3). The collinearity analysis indicated that several NAT gene loci were highly conserved between the At and Dt sub-genomes. A total of 35 gene pairs were investigated, and 34 pairs were segmental duplication and 1 pair were tandem duplication (Additional file 3: Table S3). The duplication events resulted in the amplification of GhNAT in cotton genome.

Fig. 3

Collinearity and gene duplication analysis of NAT genes in Gossypium hirsutum

Gene structure and conserved motifs analysis of GhNATs

Gene structure and protein motifs distribution have been analyzed for the evolutionary relationship among diverse gene family members in G. hirsutum (Fig. 4). Twenty conserved motifs were identified in NAT proteins. There were conserved protein motifs distributed in all GhNAT proteins. The number of motifs ranged from 1 to 17 in each protein with similar arrangements of protein motifs on same group. These distribution patterns illustrated that all GhNATs had at least one conserved protein motif . The composition of specific conserved motifs was found in particular groups, which suggested that the distribution of motifs might correlated with functional specificity. The motif 1–9 were found in the GhNAT members except Gh_D05G262700 and Gh_A07G067200. As for these motifs, they were highly conserved.

Fig. 4

Phylogenetic analysis, conserved motifs and gene structures of GhNAT genes. A Phylogenetic tree of GhNAT genes. B Conserved motifs of GhNAT proteins. Twenty conserved motifs are represented by different color boxes. C Exon–intron organization analyses of GhNAT genes. Yellow boxes mean Untranslated Regions (UTR), Exons and introns are distinguished by green boxes and black lines, respectively

The NAT genes contained 10∼15 exons in G. hirsutum, except Gh_D05G262700 (3 exons) and Gh_A07G067200 (6 exons). Intron and exon structure had similar permutation within the same group. The comprehensive illustration showed exon–intron different distribute among the GhNAT genes among various groups. Taken together, the gene structure of NAT genes had a strong relationship with gene evolution, but its mechanism was not clear, needing further study.

Promoter analysis of GhNATs genes

Promoters were strongly associated with the gene expression patterns and gene function (Xue et al. 2008). In order to predict the function of NAT gene family, the upstream cis-acting element presented in promoter regions was analyzed, which was found to be related to plant hormones (Abscisic acid, gibberellin, salicylic acid, auxin, MeJA) and abiotic stress (drought, defense and stress, low-temperature responsiveness) (Fig. 5; Additional file 4: Table S4). The distribution of cis-acting elements was diversified among different NAT genes. Hormones responsive elements were inspected on all genes. For example, MeJA regulation was found in more than half of NAT genes, reported that MeJA existed extensively in plants and was closely connection with stress resistance (Yu et al. 2009). GhNAT12 contained drought, abscisic acid, MeJA, gibberellin, salicylic acid, defense, and low-temperature responsive element . In general, majority of NAT promoters contain sequence features associated with drought, MeJA, abscisic acid, salicylic acid, defense, and stress and low-temperature response. This confirmed our guess that various cis-acting elements played very important roles in response to abiotic stress.

Fig. 5

Analysis cis-elements in promoters of GhNAT family

Expression analysis of GhNATs genes

Through exploring the expression pattern, we detected expression level of NAT genes under salt, PEG, cold, and heat stress in different periods (1 h, 3 h, 6 h, 12 h) by RNA-seq data (Additional file 5: Table S5). The gene expression under different stress conditions showed that the GhNAT members were related in the regulation of abiotic stress. The results confirmed that different genes showed different expression trends. The expression levels of three genes (Gh_A06G015500, Gh_D06G014600, Gh_D05G262700) were low to high under salt, PEG, cold, and heat stresses, and the expression level peaked at 12 h (Fig. 6). The expression pattern was roughly similar on the same group of genes, but there were slight differences among gene expression under cold and heat stress. Gh_A12G303000 and Gh_D12G296700 were significantly highly expressed in all periods of cold, heat, salt, and drought. Gh_A06G015500, Gh_D06G014600, and Gh_D05G262700 showed continuous high expression levels under four different stress conditions, and the expression level was high at 12 h. The similar trend of the NAT genes expression were detected under PEG and salt stress. Likewise, the expression pattern of NAT12 genes (Gh_A07G117800, Gh_D07G114500) were gradually increased under salt stress, and peaked at 12 h. In brief, GhNAT genes played an important role in response to plant hormones and abiotic stress, and can provide important basis for gene function analysis.

Fig. 6

Differentially expressed GhNAT genes under cold, heat, salt and PEG stress conditions.

To further confirm the expression levels of the GhNATs under drought and salt stresses, qRT-PCR was performed using the leaves of upland cotton Zhong9807 and H177, which were treated with 200 mmol·L⁻¹ NaCl and 12% PEG6000, respectively (Fig. 7). According to the multiple sequence analysis, the GhNAT genes were classified into four groups, similarly, different expression levels of the genes also were divided into four clades. The result showed that most of NAT genes were upregulated after salt and PEG treatment, while only a few genes were downregulated in upland cotton. For example, the GhNAT12 (Gh_A07G117800, Gh_D07G114500) expression level was generally up-regulated and peaked at 12 h under the salt and drought stresses. Gh_A03G078200, Gh_A03G166200, Gh_A06G015500 and Gh_D06G014600 showed continuously high expression level in generally and were upregulated at 12 h under salt and drought stress conditions.

Fig. 7

Expression pattern of GhNAT genes in response to abiotic stresses by qRT-PCR. A The expression level of GhNATs in leaves of Zhong9807 under 0 and 200 mmol·L⁻¹ NaCl treatment. B The expression level of GhNATs in the leaves of H177 under 0 and 12% PEG6000 treatment

Silencing GhNAT12 reduced the resistance of cotton to abiotic stress

To further investigate the role of GhNAT12 under abiotic stress, virus-induced gene silencing (VIGS) was performed in Zhong9807 and H177. When the albino phenotype appeared on the leaves at about 3 weeks on TRV:PDS plants (Fig. 8), the gene silencing efficiency of TRV:00 and TRV:GhNAT12 plants was confirmed by qRT-PCR. The results showed that GhNAT12 expression was significantly decreased in the silenced plants of Zhong9807 compared with TRV:00 plants (Fig. 8B), and GhNAT12 expression was also significantly decreased in the TRV:GhNAT12 plants of H177 than that in TRV:00 plants (Fig. 8D), which indicated that the gene silencing of GhNAT12 was successful in TRV:GhNAT12 plants. Subsequently, the gene-silenced plants were treated with 200 mmol·L⁻¹ NaCl and 12% PEG6000 at the three leaf-stage in Zhong9807 and H177, respectively. The result showed that the leaves were not wilting in CK plant treated with water, while, wilting phenotype of leaves began to appear after 24 h under treatment in TRV:GhNAT12 and TRV:00 plants. But the TRV:GhNAT12 plants displayed more severe withered phenotype than the TRV:00 plants, especially after 48 h. It suggested that the GhNAT12 gene played an active role in regulating plant resistance to various stresses.

Fig. 8

The phenotype of cotton leaves of GhNAT12 silenced Zhong9807 and H177 under NaCl and PEG6000 treatment, respectively. A Phenotype of cotton leaves of GhNAT12 silenced Zhong9807, the CK was treated with 0 mmol·L⁻¹ NaCl, and TRV:00 and TRV:GhNAT12 treated with 200 mmol·L⁻¹ NaCl. B GhNAT12 gene silence efficiency detection in Zhong9807. C Phenotype of cotton leaves of GhNAT12 silenced in H177, CK was treated with 0% PEG6000, and TRV: 00 and TRV: GhNAT12 treated with 12% PEG6000. D GhNAT12 gene silence efficiency detection in H177

Subcellular localization of GhNAT12

To experimentally confirm the GhNAT12 protein localization, we constructed a GhNAT12-GFP vector. This vector was transiently expressed in tobacco leave cells and onion epidermal cells. According to the fluorescence signal, the GhNAT12 protein was present in the nucleus and cell membrane (Fig. 9). Meanwhile, GhNAT12-GFP protein was detected on the plasma membrane in tobacco cells. In addition, the experiment of plasmolysis was conducted on onion epidermal cells. The same result appeared that the GhNAT12-GFP fluorescence signal was located on the cell membrane before and after plasmolysis.

Fig. 9

Subcellular localization of GhNAT12. A The GhNAT12-GFP signals were localized to the plasma membrane. B GhNAT12-GFP and GFP signals on the plasmolysis of onion cells

Discussion

Cotton is cultivated worldwide, as an important cash crop, is facing severe biotic and abiotic stresses when they grow and develop under natural conditions. Although cotton is a relatively salt-tolerant, thermophilic and drought-resistant species, the growth and development of this plant can still be greatly affected by adverse salt and drought conditions (Zhang et al. 2016). So breeders focused on key molecular factors involved in salt and drought stress response and attempted to develop salt-tolerant cotton varieties. The nucleobase–ascorbate transporter gene family was named for its transport of ascorbic acid in mammals (Liang et al. 2001), which had critical functions in many biological processes involved in the plant growth and development. AtNAT3 and AtNAT12 are mainly involved in the transport of adenine, guanine, uracil, and hypoxanthine, which play an important role in maintaining normal physiological metabolism in Arabidopsis thaliana (Hunt 2013; Niopek-Witz et al. 2014). Overexpression of MdNAT7 increased the concentrations of xanthine and uric acid in apple, leading to enhanced tolerance to salinity stress (Sun et al. 2021).

The evolutionary process of the NAT gene family lead to intriguing functional diversity and broad expansion (De Koning and Diallinas 2000; Frillingos 2012). It is very intriguing that the mammalian L-ascorbate transporters seem to have evolved from uric acid/xanthine transporters of lower eukaryotes, since uric acid and xanthine have entirely different formulas compared with ascorbic acid (Gournas et al. 2008). Several studies of NAT genes had been focused on Arabidopsis, tomato, apple, maize, and pepper. However, cotton was still lacking for researches about NATs. With the development of cotton genome sequencing, it is conceivable to investigate thoroughly on cotton NAT genes and study its potential functions. Based on the genome-wide characterization of the NAT gene family, 32, 32, 18, and 16 NAT genes were determined and characterized in four sequenced cotton species G. hirsutum, G. barbadense, G. raimondii, and G. arboreum, respectively. This result indicated that the loss of NAT genes appeared in the allotetraploid G. hirsutum and G. barbadense, and these NAT genes were conserved during the evolutionary process in cotton. The allotetraploid cotton evolved from two kinds of diploid cotton containing an A-genome (G. arboreum) and D-genome (G. raimondii). The number of genes in the allotetraploid cotton was twice that of diploid cotton implying that NAT homologs are evolutionarily conserved. And it was consisted with high rates of gene loss in the allotetraploid plants (Paterson et al. 2012; Zhang et al. 2015).

In present study, the phylogenetic tree has been constructed for 110 NAT genes from four cotton species and Arabidopsis. These NATs were divided into four distinct groups, i.e. group I, II, III and IV. It was similar to those already described for Arabidopsis, apple, maize, and tomato family members (Maurino et al. 2006; Cai et al. 2014; Sun et al. 2016). The NAT family is one of the five known groups that utilize nucleobases as their principal substrates. They belong to an evolutionarily widespread family of transport proteins in prokaryotes, fungi, plants, and mammals (De Koning and Diallinas 2000; Frillingos 2012). In addition, the number of genes in group I was the largest among different species, and was the most complex NATs. It has been previously reported that ZmLpe1 derived from group I, and characterized as a unique transporter for xanthine and uric acid (Argyrou et al. 2001). This has indicated that the substrate of most plant NATs maybe the nucleobase.

In terms of the conserved protein motifs and gene structure, most NAT genes from the same group share the similar exon–intron structure and conserved motifs in G. hirsutum. It implies that both function and structure of NATs remain conserved during evolution in the same group. Obviously, exon–intron structure and conserved motifs are slightly different among NAT gene members, and it may be responsible for their respective functional specificity. In general, this phenomenon suggests that exon–intron structure and conserved motifs have a vital role in the distinctive function. And during evolution, gene fusions or chromosomal rearrangement occurr that enlarge the NAT domain, ultimately producing the typical domain (Chai et al. 2018). The gene structure of GhD02G227100.1, GhA03G166200.1 and GhD02G184100.1 contain large intron, it worth further investigation of whether transposon insertion events have occurred. According to the gene expression profile, those three genes' expression level were relatively low, and the biological meaning needs further study. As for the chromosome position, the uneven distribution of NAT genes was displayed on specific chromosomes in At and Dt sub-genomes. The distribution pattern on the two sub-genomes tend to be the same. However, different distribution of some genes might be lost or gained compared with At and Dt sub-genomes. According to the collinearity analysis, there were 34 pairs of segmental duplication and 1 pair of tandem duplication in G. hirsutum, and they played a crucial role in the expansion of the gene family. According to the previously reported findings, one of the main drivers of the genome evolution is gene duplication (Moore and Purugganan 2003). Tandem duplication, segmental duplication, and whole-genome duplication played a crucial role in the expansion of gene family (Xu et al. 2012).

When plants are threatened by abiotic stresses, cis-acting elements played an important role (Nakashima et al. 2014). It was consistent with the previous research that similar cis-acting elements in promoter regions had relevant function (Fan et al. 2021), and the NAT genes might be associated with various physiological and biochemical processes refer to previous studies. The cis-acting elements of the NAT family contained stimulating phytohomones (abscisic acid, gibberellin, salicylic acid, auxin, MeJA) and various stresses (drought, defense and stress, low-temperature responsiveness), these results indicated that NAT genes not only participated in multiple signaling pathways but also took part in plant growth, development and defensive responses. In addition, qRT-PCR analysis was used to verify the results of the transcriptome, they were generally the same in the upregulation or downregulation. Some differences may be related to experimental conditions. The gene expression profile provides important clues for GhNAT genes in response to abiotic stress. For example, among all the 14 NAT genes in apple, only MdNAT6 proved responsive to both drought and salinity (Sun et al. 2016).

In this study, it is proved that GhNAT12 gene played an active role in regulating plant resistance to salt and drought stress. Also GhNAT12 was detected in the plasma membrane, which was consistent with the discovered localization of AtNAT12, AtNAT7 and AtNAT8 in the plasma membrane (Maurino et al. 2006). The allocation of NATs in different clades correlates with their expression during the life cycle of Arabidopsis. Some of the members of this gene family show unique expression (AtNAT12), while the expression of other AtNAT genes is restricted to specific tissues (AtNAT7, AtNAT8, AtNAT9) (Maurino et al. 2006; Niopek-Witz et al. 2014). Interestingly, these genes were in cluster I. In addition, MdNAT7 overexpression in transgenic apple plants improved their tolerance to salinity stress compared with non-transgenic plants, while opposite phenotypes were observed for MdNAT7 RNAi plants (Sun et al. 2021).

Conclusions

In this study, a comprehensive analysis of NAT gene family was performed in cotton. A total of 98 NAT genes were identified in four cotton species, including 32 genes in G. hirsutum. These genes were classified into four groups in the phylogenetic tree. Chromosomal location and collinearity analysis illustrated segmental duplication and tandem duplication might play a vital role in the expansion of the NAT gene family. Conserved motifs and gene structure analysis demonstrated evolutionary difference and conservation. The expression patterns suggested that the NAT family genes were associated with plant response to various adversity. Further, it was revealed that the GhNAT12 gene played an important role in regulating plant resistance to salt and drought stress. The present study lays a foundation for further study to explore the detailed present function of the NAT genes in cotton.