Comprehensive proteomic analysis revealing multifaceted regulatory network of the xero-halophyte Haloxylon salicornicum involved in salt tolerance

Early-responsive molecular signatures associated with halophytic adaptation in Sesuvium portulacastrum (L.)

Sesuvium portulacastrum (L.) is a halophyte, adapted to grow naturally under saline environments. The ability to use Na and K interchangeably indicated its facultative halophyte nature. No significant growth reduction occurs in seedlings up to 250 mM NaCl, except for curling of the youngest leaf. Within 8 h of salt treatment, seedlings accumulate proline, glycine betaine and other amino acids in both root and shoot. Despite a continued increase of tissue Na content, the number of differentially expressed genes (DEGs) decreases between 8 and 24 h of salt exposure, indicating transcriptional restoration after the initial osmotic challenge. At 8 h, upregulated genes mainly encode transporters and transcription factors, while genes in growth-related pathways such as photosynthesis and ribosome-associated biogenesis are suppressed. Overexpression of SpRAB18 (an ABA-responsive dehydrin), one of the most strongly induced DEGs, in soybean was found to increase biomass in control conditions and the growth benefit was maintained when plants were grown in 100 mM NaCl, indicating conservation of function in halophyte and glycophyte. An open-access transcriptome database "SesuviumKB" (https://cb.imsc.res.in/sesuviumkb/) was developed to involve the scientific community in wide-scale functional studies of S. portulacastrum genes, that could pave the way to engineer salt tolerance in crops.

The Deletion of LeuRS Revealed Its Important Roles in Osmotic Stress Tolerance, Amino Acid and Sugar Metabolism, and the Reproduction Process of Aspergillus montevidensis

Aspergillus montevidensis is an important domesticated fungus that has been applied to produce many traditional fermented foods under high osmotic conditions. However, the detailed mechanisms of tolerance to osmotic stress remain largely unknown. Here, we construct a target-deleted strain (ΔLeuRS) of A. montevidensis and found that the ΔLeuRS mutants grew slowly and suppressed the development of the cleistothecium compared to the wide-type strains (WT) under salt-stressed and non-stressed conditions. Furthermore, differentially expressed genes (p < 0.001) governed by LeuRS were involved in salt tolerance, ABC transporter, amino acid metabolism, sugar metabolism, and the reproduction process. The ΔLeuRS strains compared to WT strains under short- and long-term salinity stress especially altered accumulation levels of metabolites, such as amino acids and derivatives, carbohydrates, organic acids, and fatty acids. This study provides new insights into the underlying mechanisms of salinity tolerance and lays a foundation for flavor improvement of foods fermented with A. montevidensis.

Transcriptome and Proteome Association Analysis to Screen Candidate Genes Related to Salt Tolerance in Reaumuria soongorica Leaves under Salt Stress

This work aims at studying the molecular mechanisms underlying the response of Reaumuria soongorica to salt stress. We used RNA sequencing (RNA-Seq) and Tandem Mass Tag (TMT) techniques to identify differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in R. soongorica leaves treated with 0, 200, and 500 mM NaCl for 72 h. The results indicated that compared with the 0 mM NaCl treatment group, 2391 and 6400 DEGs were identified in the 200 and 500 mM NaCl treatment groups, respectively, while 47 and 177 DEPs were also identified. Transcriptome and proteome association analysis was further performed on R. soongorica leaves in the 0/500 mM NaCl treatment group, and 32 genes with consistent mRNA and protein expression trends were identified. SYP71, CS, PCC13-62, PASN, ZIFL1, CHS2, and other differential genes are involved in photosynthesis, vesicle transport, auxin transport, and other functions of plants, and might play a key role in the salt tolerance of R. soongorica. In this study, transcriptome and proteome association techniques were used to screen candidate genes associated with salt tolerance in R. soongorica, which provides an important theoretical basis for understanding the molecular mechanism of salt tolerance in R. soongorica and breeding high-quality germplasm resources.

Salinity-induced changes in plastoquinone pool redox state in halophytic Mesembryanthemum crystallinum L

We have analyzed the effect of salinity on photosystem II (PSII) photochemistry and plastoquinone (PQ) pool in halophytic Mesembryanthemum crystallinum plants. Under prolonged salinity conditions (7 or 10 days of 0.4 M NaCl treatment) we noted an enlarged pool of open PSII reaction centers and increased energy conservation efficiency, as envisaged by parameters of the fast and slow kinetics of chlorophyll a fluorescence. Measurements of oxygen evolution, using 2,6-dichloro-1,4-benzoquinone as an electron acceptor, showed stimulation of the PSII activity due to salinity. In salt-acclimated plants (10 days of NaCl treatment), the improved PSII performance was associated with an increase in the size of the photochemically active PQ pool and the extent of its reduction. This was accompanied by a rise in the NADP⁺/NADPH ratio. The presented data suggest that a redistribution of PQ molecules between photochemically active and non-active fractions and a change of the redox state of the photochemically active PQ pool indicate and regulate the acclimation of the photosynthetic apparatus to salinity.

A comprehensive analysis of transcriptomic data for comparison of plants with different photosynthetic pathways in response to drought stress

The main factor leading to a decrease in crop productivity is abiotic stresses, particularly drought. Plants with C4 and CAM photosynthesis are better adapted to drought-prone areas than C3 plants. Therefore, it is beneficial to compare the stress response of plants with different photosynthetic pathways. Since most crops are C3 and C4 plants, this study focused on conducting an RNA-seq meta-analysis to investigate and compare how C3 and C4 plants respond to drought stress at the gene expression level in their leaves. Additionally, the accuracy of the meta-analysis results was confirmed with RT-qPCR. Based on the functional enrichment and network analysis, hub genes related to ribosomal proteins and photosynthesis were found to play a potential role in stress response. Moreover, our findings suggest that the low abundant amino acid degradation pathway, possibly through providing ATP source for the TCA cycle, in both groups of plants and the activation of the OPPP pathway in C4 plants, through providing the electron source required by this plant, can help to improve drought stress tolerance.

Intensity and duration of salinity required to form adaptive response in C4 halophyte Kochia prostrata (L.) Shrad

Plant adaptation to salinity is a highly multifaceted process, harnessing various physiological mechanisms depending on the severity and duration of salt stress. This study focuses on the effects of 4- and 10-day treatments with low (100 mM NaCl) and moderate (200 mM NaCl) salinity on growth, CO₂/H₂O gas exchange, stomatal apparatus performance, the efficiency of photosystems I and II (PS I and II), content of key C₄ photosynthesis enzymes, and the accumulation of Na⁺, K⁺, and proline in shoots of the widespread forage C₄ halophyte Kochia prostrata. Our data show that 4 days of low salinity treatment resulted in a decrease in biomass, intensity of apparent photosynthesis, and cyclic electron transport around PS I. It was accompanied by an increase in transpiration and Rubisco and PEPC contents, while the Na⁺ and proline contents were low in K. prostrata shoots. By the 10th day of salinity, Na⁺ and proline have accumulated; PS I function has stabilized, while PS II efficiency has decreased due to the enhanced non-photochemical quenching of chlorophyll fluorescence (NPQ). Thus, under low salinity conditions, Na⁺ accumulated slowly and the imbalance between light and dark reactions of photosynthesis was observed. These processes might be induced by an early sodium signaling wave that affects cellular pH and ion homeostasis, ultimately disturbing photosynthetic electron transport. Another adaptive reaction more "typical" of salt-tolerant species was observed at 200 mM NaCl treatment. It proceeds in two stages. First, during the first 4 days, dry biomass and apparent photosynthesis decrease, whereas stomata sensitivity and dissipation energy during dark respiration increase. In parallel, an active Na⁺ accumulation and a decreased K⁺/Na⁺ ratio take place. Second, by the 10th day, a fully-fledged adaptive response was formed, when growth and apparent photosynthesis stabilized and stomata closed. Decreased dissipation energy, increased WUE, stabilization of Rubisco and PEPC contents, and decreased proline content testify to the completion of the adaptation and stabilization of the physiological state of plants. The obtained results allowed us to conclude that the formation of a full-fledged salt-tolerant response common for halophytes in K. prostrata occurs by the 10th day of moderate salinity.

Identification of key genes contributing to amino acid biosynthesis in Torreya grandis using transcriptome and metabolome analysis

Torreya grandis has high economic and nutritional value due to the high nutrients in its kernels. The kernels of different development stages vary enormously in their amino acids content. However, the molecular basis and the regulatory mechanism of amino acid biosynthesis remain unclear. Here, transcriptome and metabolome analysis were performed. Correlation analysis result showed that 4 unigenes were significantly and positively correlated with at least 10 amino acids. The full length CDS of 2 unigenes (TgDAHP2 and TgASA1) were successfully cloned from the 4 unigenes for DAHP, ASA and CITS. Subcelluar localization analysis showed that both TgDAHP2 and TgASA1 were localized to the chloroplast. Overexpression of TgDAHP2 and TgASA1 in Arabidopsis can greatly increase the content of most amino acids. Moreover, 3 transcription factors were found to positively regulate the expression of TgASA1. This research contributes to understand the molecular regulatory mechanisms of amino acid biosynthesis in T. grandis.

Changes in leaf ecophysiological traits and proteome profile provide new insights into variability of salt response in the succulent halophyte Cakile maritima

Natural variability of stress tolerance in halophytic plants is of significance both ecologically and in view of identifying molecular traits for salt tolerance in plants. Using ecophysiological and proteomic analyses, we address these phenomena in two Tunisian accessions of the oilseed halophyte, Cakile maritima Scop., thriving on arid and semi-arid Mediterranean bioclimatic stages (Djerba and Raoued, respectively), with a special emphasis on the leaves. Changes in biomass, photosynthetic gas exchange and pigment concentrations in C. maritima plants treated with three salinity levels (0, 100 and 300mM NaCl) were monitored for 1month. Comparative two-dimensional gel electrophoresis (2-DE) revealed 94 and 56 proteins of differential abundance in Raoued and Djerba accessions, respectively. These salinity-responsive proteins were mainly related to photosynthesis and oxidative phosphorylation (OXPHOS). Although Djerba accession showed a lower biomass productivity, it showed a slightly higher CO2 assimilation rate than Raoued accession when salt-treated. Photosynthesis impairment in both accessions under salinity was also suggested by the lower abundance of proteins involved in Calvin cycle and electron transfer. A significant increase of protein spots involved in the OXPHOS system was found in Djerba accession, suggesting an increase in mitochondrial respiration for increased ATP production under saline conditions, whereas a lesser pronounced trend was observed for Raoued accession. The latter showed in addition higher abundance of proteins involved in photorespiration. Salt-challenged plants of Djerba also likely developed mechanisms for scavenging ROS in leaves as shown by the increase in superoxide dismutase and thioredoxin, while an opposite trend was found in Raoued.

Physiological response and proteomics analysis of Reaumuria soongorica under salt stress

Soil salinity can severely restrict plant growth. Yet Reaumuria soongorica can tolerate salinity well. However, large-scale proteomic studies of this plant’s response to salinity have yet to reported. Here, R. soongorica seedlings (4 months old) were used in an experiment where NaCl solutions simulated levels of soil salinity stress. The fresh weight, root/shoot ratio, leaf relative conductivity, proline content, and total leaf area of R. soongorica under CK (0 mM NaCl), low (200 mM NaCl), and high (500 mM NaCl) salt stress were determined. The results showed that the proline content of leaves was positively correlated with salt concentration. With greater salinity, the plant fresh weight, root/shoot ratio, and total leaf area increased initially but then decreased, and vice-versa for the relative electrical conductivity of leaves. Using iTRAQ proteomic sequencing, 47 177 136 differentially expressed proteins (DEPs) were identified in low-salt versus CK, high-salt versus control, and high-salt versus low-salt comparisons, respectively. A total of 72 DEPs were further screened from the comparison groupings, of which 34 DEPs increased and 38 DEPs decreased in abundance. These DEPs are mainly involved in translation, ribosomal structure, and biogenesis. Finally, 21 key DEPs (SCORE value ≥ 60 points) were identified as potential targets for salt tolerance of R. soongolica. By comparing the protein structure of treated versus CK leaves under salt stress, we revealed the key candidate genes underpinning R. soongolica’s salt tolerance ability. This works provides fresh insight into its physiological adaptation strategy and molecular regulatory network, and a molecular basis for enhancing its breeding, under salt stress conditions.

Integrated physiological and comparative proteomics analysis of contrasting genotypes of pearl millet reveals underlying salt-responsive mechanisms

Salinity stress poses a significant risk to plant development and agricultural yield. Therefore, elucidation of stress-response mechanisms has become essential to identify salt-tolerance genes in plants. In the present study, two genotypes of pearl millet (Pennisetum glaucum L.) with contrasting tolerance for salinity exhibited differential morpho-physiological and proteomic responses under 150 mM NaCl. The genotype IC 325825 was shown to withstand the stress better than IP 17224. The salt-tolerance potential of IC 325825 was associated with its ability to maintain intracellular osmotic, ionic, and redox homeostasis and membrane integrity under stress. The IC 325825 genotype exhibited a higher abundance of C4 photosynthesis enzymes, efficient enzymatic and non-enzymatic antioxidant system, and lower Na⁺ /K⁺ ratio compared with IP 17224. Comparative proteomics analysis revealed greater metabolic perturbation in IP 17224 under salinity, in contrast to IC 325825 that harbored pro-active stress-responsive machinery, allowing its survival and better adaptability under salt stress. The differentially abundant proteins were in silico characterized for their functions, subcellular-localization, associated pathways, and protein-protein interaction. These proteins were mainly involved in photosynthesis/response to light stimulus, carbohydrate and energy metabolism, and stress responses. Proteomics data were validated through expression profiling of the selected genes, revealing a poor correlation between protein abundance and their relative transcript levels. This study has provided novel insights into salt adaptive mechanisms in P. glaucum, demonstrating the power of proteomics-based approaches. The critical proteins identified in the present study could be further explored as potential objects for engineering stress tolerance in salt-sensitive major crops.

Stability of thylakoid protein complexes and preserving photosynthetic efficiency are crucial for the successful recovery of the halophyte Cakile maritima from high salinity

Plants native to extreme habitats often face changes in environmental conditions such as salinity level and water availability. In response, plants have evolved efficient mechanisms allowing them to survive or recover. In the present work, effects of high salinity and salt-stress release were studied on the halophyte Cakile maritima. Four week-old plants were either cultivated at 0 mM NaCl or 200 mM NaCl. After one month of treatment, plants were further irrigated at either 0 mM NaCl, 200 mM NaCl, or rewatered to 0 mM NaCl (stress release). Upon salt stress, C. maritima plants exhibited reduced biomass production and shoot hydration which were associated with a decrease in the amount of chlorophyll a and b. However, under the same stressful conditions a significant increase of anthocyanin and malonyldialdehyde concentrations was noticed. Salt-stressed plants were able to maintain stable protein complexes of thylakoid membranes. Measurement of chlorophyll fluorescence and P700 redox state showed that PSI was more susceptible for damage by salinity than PSII. PSII machinery was significantly enhanced under saline conditions. All measured parameters were partially restored under salt-stress release conditions. Photoinhibition of PSI was also reversible and C. maritima was able to successfully re-establish PSI machinery indicating the high contribution of chloroplasts in salt tolerance mechanisms of C. maritima. Overall, to overcome high salinity stress, C. maritima sets a cascade of physio-biochemical and molecular pathways. Chloroplasts seem to act as metabolic centers as part of this adaptive process enabling growth restoration in this halophyte following salt stress release.