Identification and analysis of the chloride channel gene family members in tobacco (Nicotiana tabacum)

The Role of Chloride Channels in Plant Responses to NaCl

Chloride (Cl-) is considered a crucial nutrient for plant growth, but it can be a challenge under saline conditions. Excessive accumulation of Cl- in leaves can cause toxicity. Chloride channels (CLCs) are expressed in the inner membranes of plant cells and function as essential Cl- exchangers or channels. In response to salt stress in plants, CLCs play a crucial role, and CLC proteins assist in maintaining the intracellular Cl- homeostasis by sequestering Cl- into vacuoles. Sodium chloride (NaCl) is the primary substance responsible for causing salt-induced phytotoxicity. However, research on plant responses to Cl- stress is comparatively rare, in contrast to that emphasizing Na+. This review provides a comprehensive overview of the plant response and tolerance to Cl- stress, specifically focusing on comparative analysis of CLC protein structures in different species. Additionally, to further gain insights into the underlying mechanisms, the study summarizes the identified CLC genes that respond to salt stress. This review provides a comprehensive overview of the response of CLCs in terrestrial plants to salt stress and their biological functions, aiming to gain further insights into the mechanisms underlying the response of CLCs in plants to salt stress.

Genome-wide analysis of long noncoding RNAs in response to salt stress in Nicotiana tabacum

BACKGROUND

Long noncoding RNAs (lncRNAs) have been shown to play important roles in the response of plants to various abiotic stresses, including drought, heat and salt stress. However, the identification and characterization of genome-wide salt-responsive lncRNAs in tobacco (Nicotiana tabacum L.) have been limited. Therefore, this study aimed to identify tobacco lncRNAs in roots and leaves in response to different durations of salt stress treatment.

RESULTS

A total of 5,831 lncRNAs were discovered, with 2,428 classified as differentially expressed lncRNAs (DElncRNAs) in response to salt stress. Among these, only 214 DElncRNAs were shared between the 2,147 DElncRNAs in roots and the 495 DElncRNAs in leaves. KEGG pathway enrichment analysis revealed that these DElncRNAs were primarily associated with pathways involved in starch and sucrose metabolism in roots and cysteine and methionine metabolism pathway in leaves. Furthermore, weighted gene co-expression network analysis (WGCNA) identified 15 co-expression modules, with four modules strongly linked to salt stress across different treatment durations (MEsalmon, MElightgreen, MEgreenyellow and MEdarkred). Additionally, an lncRNA-miRNA-mRNA network was constructed, incorporating several known salt-associated miRNAs such as miR156, miR169 and miR396.

CONCLUSIONS

This study enhances our understanding of the role of lncRNAs in the response of tobacco to salt stress. It provides valuable information on co-expression networks of lncRNA and mRNAs, as well as networks of lncRNAs-miRNAs-mRNAs. These findings identify important candidate lncRNAs that warrant further investigation in the study of plant-environment interactions.

MhCLC-c1, a Cl channel c homolog from Malus hupehensis, alleviates NaCl-induced cell death by inhibiting intracellular Cl- accumulation

BACKGROUND

Overaccumulation of chloride (Cl) when plants suffer NaCl causes cell damage and death, and is regulated by Cl^- channel protein (CLC). Apple roots are very sensitive to Cl^-, but information associated with CLC is limited in apple crop that widely cultivated in the world.

RESULTS

We identified 9 CLCs from the apple genome and divided them into two subclasses. Among them, MdCLC-c1 promoter contained the largest number of cis-acting elements associated with NaCl stress, and only the MdCLC-c1, MdCLC-d, and MdCLC-g were predicted that may be Cl^- antiporters or channels. Expression analysis of MdCLCs homologs in the roots of Malus hupehensis showed that most of the MhCLCs expression were response to NaCl stress, especially MhCLC-c1 expression was upregulated continuously and rapidly expressed during NaCl treatment. Therefore, we isolated MhCLC-c1 and observed it was a plasma membrane-localized protein. The MhCLC-c1 suppression significantly increased sensitivity, reactive oxygen species content, and cell death of apple calli; while MhCLC-c1 overexpression decreased sensitivity, reactive oxygen species content, and cell death of apple calli and Arabidopsis by inhibiting intracellular Cl^- accumulation under NaCl stress.

CONCLUSIONS

The study selected and isolated a CLC-c gene MhCLC-c1 from Malus hupehensis based on identification of CLCs gene family in apple, and their homologs MhCLCs expression patterns during NaCl treatments, revealing that MhCLC-c1 alleviates NaCl-induced cell death by inhibiting intracellular Cl^- accumulation. Our findings confer the comprehensive and in-depth upstanding of the mechanism that plants resist salt stress, and might also confer genetic improvement of salt tolerance in horticultural crops and the development and utilization of saline-alkali land.

Genome-wide identification and characterization of NPF family reveals NtNPF6.13 involving in salt stress in Nicotiana tabacum

Proteins of the Nitrate Transporter 1/Peptide Transporter (NPF) family transport a diverse variety of substrates, such as nitrate, peptides, hormones and chloride. In this study, a systematic analysis of the tobacco (Nicotiana tabacum) NPF family was performed in the cultivated 'K326'. In total, 143 NtNPF genes were identified and phylogenetically classified into eight subfamilies, NPF1 to NPF8, based on the classification of NPF families in other plant species. The chromosomal locations and structures of the NtNPF genes were analyzed. The expression profiles of NtNPF genes under NaCl stress were analyzed to screen the possible NPF genes involving in chloride regulation in tobacco. Most NtNPF6 genes responded to salt stress in the roots and leaves. The expression of NtNPF6.13 was significantly down-regulated after salt stress for 12h. The chloride content was reduced in the roots of ntnpf6.13 mutant. These findings support the participation of NtNPF6.13 in chloride uptake. Several other NtNPF genes that play potential roles in chloride metabolism of tobacco require further study.

Genome-Wide Identification and Functional Characterization of the Chloride Channel TaCLC Gene Family in Wheat (Triticum aestivum L.)

In plants, chloride channels (CLC) are involved in a series of specific functions, such as regulation of nutrient transport and stress tolerance. Members of the wheat Triticum aestivum L. CLC (TaCLC) gene family have been proposed to encode anion channels/transporters that may be related to nitrogen transportation. To better understand their roles, TaCLC family was screened and 23 TaCLC gene sequences were identified using a Hidden Markov Model in conjunction with wheat genome database. Gene structure, chromosome location, conserved motif, and expression pattern of the resulting family members were then analyzed. Phylogenetic analysis showed that the TaCLC family can be divided into two subclasses (I and II) and seven clusters (-a, -c1, -c2, -e, -f1, -f2, and -g2). Using a wheat RNA-seq database, the expression pattern of TaCLC family members was determined to be an inducible expression type. In addition, seven genes from seven different clusters were selected for quantitative real-time PCR (qRT-PCR) analysis under low nitrogen stress or salt stress conditions, respectively. The results indicated that the gene expression levels of this family were up-regulated under low nitrogen stress and salt stress, except the genes of TaCLC-c2 cluster which were from subfamily -c. The yeast complementary experiments illustrated that TaCLC-a-6AS-1, TaCLC-c1-3AS, and TaCLC-e-3AL all had anion transport functions for NO₃⁻ or Cl⁻, and compensated the hypersensitivity of yeast GEF1 mutant strain YJR040w (Δgef1) in restoring anion-sensitive phenotype. This study establishes a theoretical foundation for further functional characterization of TaCLC genes and provides an initial reference for better understanding nitrate nitrogen transportation in wheat.

CLCNt2 Mediates Nitrate Content in Tobacco Leaf, Impacting the Production of Tobacco-Specific Nitrosamines in Cured Leaves

Nitrate accumulation in tobacco (Nicotiana tabacum L.) leaf, particularly in the burley (BU) type, is a reservoir for the generation of nitrosating agents responsible for the formation of tobacco-specific nitrosamines (TSNAs). TSNAs are mainly produced via the nitrosation of alkaloids occurring during the curing of tobacco leaves. Additional formation of TSNAs may also occur during tobacco storage, leaf processing and in some circumstances via pyrosynthesis during combustion. Two TSNA species, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and N-nitrosonornicotine (NNN) are found in the tobacco products and have been documented to be animal carcinogens. A previous study showed that decreasing the accumulation of nitrate in tobacco leaf via the overexpression of a deregulated form of nitrate reductase is efficient to reduce the production of TSNAs. We pursue in finding another molecular genetic target to lower nitrate in BU tobacco. Suppressing expression or knocking-out CLCNt2 has a direct impact on leaf nitrate and TSNA reduction in cured leaves without altering biomass. This study provides now a straight path toward the development of new commercial tobacco varieties with reduced TSNA levels by breeding of variants deficient in active CLCNt2 copies.

OsPUB41, a U-box E3 ubiquitin ligase, acts as a negative regulator of drought stress response in rice (Oryza Sativa L.)

OsPUB41 plays a negative role in drought stress response through the mediation of OsUBC25 and interacts with OsCLC6, suggesting a putative substrate. The notable expansion of Plant U-Box E3 ligases (PUB), compared with those in mammals, implies that PUB proteins have evolved to perform plant-specific functions. OsPUB41, a potential ortholog of CMPG1, was recently reported to regulate the cell wall degrading enzyme (CWDE)-induced innate immune response in rice. Here, we characterized the OsPUB41 gene, which encodes a dual-localized cytosolic and nuclear U-box E3 ligase in rice. OsPUB41 expression was specifically induced by dehydration among various abiotic stresses and abscisic acid (ABA) treatments. Furthermore, we revealed that the core U-box motif of OsPUB41 possesses the E3 ligase activity that can be activated by OsUBC25 in rice. The Ubi:RNAi-OsPUB41 knock-down and ospub41 suppression mutant plants exhibited enhanced tolerance to drought stress compared with the wild-type rice plants in terms of transpirational water loss, long-term dehydration response, and chlorophyll content. Moreover, the knock-down or suppression of the OsPUB41 gene did not cause adverse effect on rice yield-related traits. Yeast two-hybrid and an in vitro pull-down analyses revealed that OsCLC6, a chloride channel, is a putative substrate of OsPUB41. Overall, these results suggest that OsPUB41 acts as a negative regulator of dehydration conditions and interacts with OsCLC6, implying that it is a substrate of OsPUB41.

Reconstruction of the full-length transcriptome of cigar tobacco without a reference genome and characterization of anion channel/transporter transcripts

BACKGROUND

Cigar wrapper leaves are the most important raw material of cigars. Studying the genomic information of cigar tobacco is conducive to improving cigar quality from the perspective of genetic breeding. However, no reference genome or full-length transcripts at the genome-wide scale have been reported for cigar tobacco. In particular, anion channels/transporters are of high interest for their potential application in regulating the chloride content of cigar tobacco growing on coastal lands, which usually results in relatively high Cl- accumulation, which is unfavorable. Here, the PacBio platform and NGS technology were combined to generate a full-length transcriptome of cigar tobacco used for cigar wrappers.

RESULTS

High-quality RNA isolated from the roots, leaves and stems of cigar tobacco were subjected to both the PacBio platform and NGS. From PacBio, a total of 11,652,432 subreads (19-Gb) were generated, with an average read length of 1,608 bp. After corrections were performed in conjunction with the NGS reads, we ultimately identified 1,695,064 open reading frames including 21,486 full-length ORFs and 7,342 genes encoding transcription factors from 55 TF families, together with 2,230 genes encoding long non-coding RNAs. Members of gene families related to anion channels/transporters, including members of the SLAC and CLC families, were identified and characterized.

CONCLUSIONS

The full-length transcriptome of cigar tobacco was obtained, annotated, and analyzed, providing a valuable genetic resource for future studies in cigar tobacco.

The chloride channels: Silently serving the plants

Chloride channels (CLCs), member of anion transporting proteins, are present ubiquitously in all life forms. Diverging from its name, the CLC family includes both channel and exchanger (proton-coupled) proteins; nevertheless, they share conserved structural organization. They are engaged in diverse indispensable functions such as acid and fluoride tolerance in prokaryotes to muscle stabilization, transepithelial transport, and neuronal development in mammals. Mutations in genes encoding CLCs lead to several physiological disorders in different organisms, including severe diseases in humans. Even in plants, loss of CLC protein function severely impairs various cellular processes critical for normal growth and development. These proteins sequester Cl^- into the vacuole, thus, making them an attractive target for improving salinity tolerance in plants caused by high abundance of salts, primarily NaCl. Besides, some CLCs are involved in NO₃ ^- transport and storage function in plants, thus, influencing their nitrogen use efficiency. However, despite their high significance, not many studies have been carried out in plants. Here, we have attempted to concisely highlight the basic structure of CLC proteins and critical residues essential for their function and classification. We also present the diverse functions of CLCs in plants from their first cloning back in 1996 to the knowledge acquired as of now. We stress the need for carrying out more in-depth studies on CLCs in plants, for they may have future applications towards crop improvement.

GhCLCg-1, a Vacuolar Chloride Channel, Contributes to Salt Tolerance by Regulating Ion Accumulation in Upland Cotton

Soil and freshwater salinization is increasingly becoming a problem worldwide and has adversely affected plant growth. However, most of the related studies have focused on sodium ion (Na⁺) stress, with relatively little research on chloride ion (Cl^-) stress. Here, we found that upland cotton (Gossypium hirsutum) plants accumulated Cl^- and exhibited strong growth inhibition under NaCl or KCl treatment. Then, a chloride channel gene (GhCLCg-1) was cloned from upland cotton. Phylogenetic and sequence analyses indicated that GhCLCg-1 was highly homologous to AtCLCg and also have conserved voltage_CLC and CBS domains. The subcellular localization assay showed that GhCLCg-1 was localized on the vacuolar membrane. Gene expression analyses revealed that the expression of GhCLCg-1 increased rapidly in cotton in response to chloride stress (NaCl or KCl), and the transcript levels increased as the chloride stress intensified. The overexpression of GhCLCg-1 in Arabidopsis thaliana changed the uptake of ions with a decrease of the Na⁺/K⁺ ratios in the roots, stems, and leaves, and enhanced salt tolerance. In contrast, silencing GhCLCg-1 in cotton plants increased the Cl^- contents in the roots, stems, and leaves and the Na⁺/K⁺ ratios in the stems and leaves, resulting in compromised salt tolerance. These results provide important insights into the toxicity of chloride to plants and also indicate that GhCLCg-1 can positively regulates salt tolerance by adjusting ion accumulation in upland cotton.

Genome-wide identification and expression analysis of the CLC gene family in pomegranate (Punica granatum) reveals its roles in salt resistance

BACKGROUNDS

Pomegranate (Punica granatum L.) is an important commercial fruit tree, with moderate tolerance to salinity. The balance of Cl^- and other anions in pomegranate tissues are affected by salinity, however, the accumulation patterns of anions are poorly understood. The chloride channel (CLC) gene family is involved in conducting Cl^-, NO₃^-, HCO₃^- and I^-, but its characteristics have not been reported on pomegranate.

RESULTS

In this study, we identified seven PgCLC genes, consisting of four antiporters and three channels, based on the presence of the gating glutamate (E) and the proton glutamate (E). Phylogenetic analysis revealed that seven PgCLCs were divided into two clades, with clade I containing the typical conserved regions GxGIPE (I), GKxGPxxH (II) and PxxGxLF (III), whereas clade II not. Multiple sequence alignment revealed that PgCLC-B had a P [proline, Pro] residue in region I, which was suspected to be a NO₃^-/H⁺ exchanger, while PgCLC-C1, PgCLC-C2, PgCLC-D and PgCLC-G contained a S [serine, Ser] residue, with a high affinity to Cl^-. We determined the content of Cl^-, NO₃^-, H₂PO₄^-, and SO₄^2- in pomegranate tissues after 18 days of salt treatments (0, 100, 200 and 300 mM NaCl). Compared with control, the Cl^- content increased sharply in pomegranate tissues. Salinity inhibited the uptake of NO₃^- and SO₄^2-, but accelerated H₂PO₄^- uptake. The results of real-time reverse transcription PCR (qRT-PCR) revealed that PgCLC genes had tissue-specific expression patterns. The high expression levels of three antiporters PgCLC-C1, PgCLC-C2 and PgCLC-D in leaves might be contributed to sequestrating Cl^- into the vacuoles. However, the low expression levels of PgCLCs in roots might be associated with the exclusion of Cl^- from root cells. Also, the up-regulated PgCLC-B in leaves indicated that more NO₃^- was transported into leaves to mitigate the nitrogen deficiency.

CONCLUSIONS

Our findings suggested that the PgCLC genes played important roles in balancing of Cl^- and NO₃^- in pomegranate tissues under salt stress. This study established a theoretical foundation for the further functional characterization of the CLC genes in pomegranate.

Genome-wide analysis of chloride channel-encoding gene family members and identification of CLC genes that respond to Cl-/salt stress in upland cotton

Chloride channels (CLCs) are kinds of anion transport protein family members that are mainly distributed in cell endomembrane systems of prokaryotic and eukaryotic organisms and mediate anion (Cl^-, as a representative) transport and homeostasis. Some CLC genes have been reported to be involved in Cl^-/salt tolerance of plants exposed to NaCl stress. Through BLAST in cotton database, a total of 22 CLCs were identified in genomes A and D in upland cotton (Gossypium hirsutum L.), and except for GhCLC6 and GhCLC17, they formed highly similar homologous genes pairs. According to the prediction in PlantCARE database, many cis-acting elements related to abiotic stress responses, including ABREs, AREs, GT-1s, G-boxes, MYBs, MYCs, etc., were found in the promoters of GhCLCs. qRT-PCR revealed that most GhCLC gene expression was upregulated in the roots and leaves of cotton seedlings under salt stress, and those of homologous GhCLC4/15, GhCLC5/16, and GhCLC7/18 displayed more obvious expression. Furthermore, according to leaf virus-induced gene silencing (VIGS) assay and compared with the salt-stressed GhCLC4/15- and GhCLC7/18-silenced cotton plants, the salt-stressed GhCLC5/16-silenced plants displayed relatively better growth with significant increases in both Cl^- content and Cl^-/NO₃^- ratio in the roots and drop of the same parameters in the leaves. These results indicate that homologous GhCLC5/16, with the highest NaCl^-induced upregulation of expression and the maximum number of MYC cis-acting elements, might be the key members contributing to cotton Cl^-/salt tolerance by regulating the transport, interaction and homeostasis of Cl^- and NO₃^-.

Genome-wide identification and expression analysis of the CLC superfamily genes in tea plants (Camellia sinensis)

The voltage-gated chloride channel (CLC) superfamily is one of the most important anion channels that is widely distributed in bacteria and plants. CLC is involved in transporting various anions such as chloride (Cl^-) and fluoride (F^-) in and out of cells. Although Camellia sinensis is a hyper-accumulated F plant, there is no studies on the CLC gene superfamily in the tea plant. Here, 8 CLC genes were identified from C. sinensis and they were named CsCLC1-8. The structure of CsCLC genes and the proteins were not conserved; the number of exons varied from 3 to 24, and the number of transmembrane domains contained 2 to 10. Furthermore, phylogenetic analysis revealed that CsCLC4-8 in subclass I contained the typical conserved domains GxGIPE (I), GKxGPxxH (II) and PxxGxLF (III), and CsCLC1-3 in subclass II did not contain any of the three conserved residues. We measured the expression levels of CsCLCs in roots, stems and leaves to assess the responses to different concentrations of Cl^- and F^-. The result indicated that CsCLCs participated in subfunctionalization in response to Cl^- and F^-, and CsCLC1-3 was more sensitive to F^- treatments than CsCLC4-8, CsCLC6 and CsCLC7 may participate in absorption and long-distance transport of Cl^-.