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

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.

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.

Effects of Arbuscular Mycorrhizal Fungus on Sodium and Chloride Ion Channels of Casuarina glauca under Salt Stress

Casuarina glauca is an important coastal protection forest species, which is exposed to high salt stress all year round. Arbuscular mycorrhizal fungi (AMF) can promote the growth and salt tolerance of C. glauca under salt stress. However, the effects of AMF on the distribution of Na⁺ and Cl^- and the expression of related genes in C. glauca under salt stress need to be further explored. This study explored the effects of Rhizophagus irregularis on plant biomass, the distribution of Na⁺ and Cl^-, and the expression of related genes in C. glauca under NaCl stress through pot simulation experiments. The results revealed that the mechanisms of Na⁺ and Cl^- transport of C. glauca under NaCl stress were different. C. glauca took a salt accumulation approach to Na⁺, transferring Na⁺ from roots to shoots. Salt accumulation of Na⁺ promoted by AMF was associated with CgNHX7. The transport mechanism of C. glauca to Cl^- might involve salt exclusion rather than salt accumulation, and Cl^- was no longer transferred to shoots in large quantities but started to accumulate in roots. However, AMF alleviated Na⁺ and Cl^- stress by similar mechanisms. AMF could promote salt dilution of C. glauca by increasing biomass and the content of K⁺, compartmentalizing Na⁺ and Cl^- in vacuoles. These processes were associated with the expression of CgNHX1, CgNHX2-1, CgCLCD, CgCLCF, and CgCLCG. Our study will provide a theoretical basis for the application of AMF to improve salt tolerance in plants.

Molecular Evolution of Plant 14-3-3 Proteins and Function of Hv14-3-3A in Stomatal Regulation and Drought Tolerance

Drought significantly affects stomatal regulation, leading to the reduced growth and productivity of plants. Plant 14-3-3 proteins were reported to participate in drought response by regulating the activities of a wide array of target proteins. However, the molecular evolution, expression pattern and physiological functions of 14-3-3s under drought stress remain unclear. In this study, a comparative genomic analysis and the tissue-specific expression of 14-3-3s revealed the highly conserved and early evolution of 14-3-3s in green plants and duplication and expansion of the 14-3-3s family members in angiosperms. Using barley (Hordeum vulgare) for the functional characterization of 14-3-3 proteins, the transcripts of five members out of six Hv14-3-3s were highly induced by drought in the drought-tolerant line, XZ141. Suppression of the expression of Hv14-3-3A through barley stripe mosaic virus-virus induced gene silencing resulted in significantly increased drought sensitivity and stomatal density as well as significantly reduced net CO2 assimilation (A) and stomatal conductance (gs) in barley. Moreover, we showed the functional interactions between Hv14-3-3s and key proteins in drought and stomatal responses in plants-such as Open Stomata 1 (HvOST1), Slow Anion Channel 1 (HvSLAC1), three Heat Shock Proteins (HvHSP90-1/2/5) and Dehydration-Responsive Element-Binding 3 (HvDREB3). Taken together, we propose that 14-3-3s are highly evolutionarily conserved proteins and that Hv14-3-3s represent a group of the core regulatory components for the rapid stomatal response to drought in barley. This study will provide important evolutionary and molecular evidence for future applications of 14-3-3 proteins in breeding drought-tolerant crops in a changing global climate.

Overexpression of Pyrus sinkiangensis HAT5 enhances drought and salt tolerance, and low-temperature sensitivity in transgenic tomato

The homeodomain-leucine zipper protein HAT belongs to the homeodomain leucine zipper subfamily (HD-Zip) and is important for regulating plant growth and development and stress tolerance. To investigate the role of HAT5 in tolerance to drought, salt, and low temperature stress, we selected a HAT gene from Pyrus sinkiangensis Yü (Pyrus sinkiangensis T.T. Yu). The sequences were analyzed using ioinformatics, and the overexpressed tomato lines were obtained using molecular biology techniques. The phenotypes, physiological, and biochemical indexes of the wild-type and transgenic tomato lines were observed under different stress conditions. We found that the gene had the highest homology with PbrHAT5. Under drought and NaCl stress, osmotic regulatory substances (especially proline) were significantly accumulated, and antioxidant enzyme activities were enhanced. The malondialdehyde level and relative electrical conductivity of transgenic tomatoes under low temperature (freezing) stress were significantly higher than those of wild-type tomatoes. The reactive oxygen species scavenging system was unbalanced. This study found that PsHAT5 improved the tolerance of tomatoes to drought and salt stress by regulating proline metabolism and oxidative stress ability, reducing the production of reactive oxygen species, and maintaining normal cell metabolism. In conclusion, the PsHAT5 transcription factor has great potential in crop resistance breeding, which lays a theoretical foundation for future excavation of effective resistance genes of the HD-Zip family and experimental field studies.

Molecular response and evolution of plant anion transport systems to abiotic stress

We propose that anion channels are essential players for green plants to respond and adapt to the abiotic stresses associated changing climate via reviewing the literature and analyzing the molecular evolution, comparative genetic analysis, and bioinformatics analysis of the key anion channel gene families. Climate change-induced abiotic stresses including heatwave, elevated CO₂, drought, and flooding, had a major impact on plant growth in the last few decades. This scenario could lead to the exposure of plants to various stresses. Anion channels are confirmed as the key factors in plant stress responses, which exist in the green lineage plants. Numerous studies on anion channels have shed light on their protein structure, ion selectivity and permeability, gating characteristics, and regulatory mechanisms, but a great quantity of questions remain poorly understand. Here, we review function of plant anion channels in cell signaling to improve plant response to environmental stresses, focusing on climate change related abiotic stresses. We investigate the molecular response and evolution of plant slow anion channel, aluminum-activated malate transporter, chloride channel, voltage-dependent anion channel, and mechanosensitive-like anion channel in green plant. Furthermore, comparative genetic and bioinformatic analysis reveal the conservation of these anion channel gene families. We also discuss the tissue and stress specific expression, molecular regulation, and signaling transduction of those anion channels. We propose that anion channels are essential players for green plants to adapt in a diverse environment, calling for more fundamental and practical studies on those anion channels towards sustainable food production and ecosystem health in the future.

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.

Genome and Transcriptome Sequencing of Populus × sibirica Identified Sex-Associated Allele-Specific Expression of the CLC Gene

Transcriptome sequencing of leaves, catkin axes, and flowers from male and female trees of Populus × sibirica and genome sequencing of the same plants were performed for the first time. The availability of both genome and transcriptome sequencing data enabled the identification of allele-specific expression. Such an analysis was performed for genes from the sex-determining region (SDR). P. × sibirica is an intersectional hybrid between species from sections Aigeiros (Populus nigra) and Tacamahaca (Populus laurifolia, Populus suaveolens, or Populus × moskoviensis); therefore, a significant number of heterozygous polymorphisms were identified in the SDR that allowed us to distinguish between alleles. In the SDR, both allelic variants of the TCP (T-complex protein 1 subunit gamma), CLC (Chloride channel protein CLC-c), and MET1 (DNA-methyltransferase 1) genes were expressed in females, while in males, two allelic variants were expressed for TCP and MET1 but only one allelic variant prevailed for CLC. Targeted sequencing of TCP, CLC, and MET1 regions on a representative set of trees confirmed the sex-associated allele-specific expression of the CLC gene in generative and vegetative tissues of P. × sibirica. Our study brings new knowledge on sex-associated differences in Populus species.