Coordination of carbon fixation and nitrogen metabolism in Salicornia europaea under salinity: Comparative proteomic analysis on chloroplast proteins

Starvation and re-feeding of Gilthead seabream (Sparus aurata) and European seabass (Dicentrarchus labrax) co-cultured with glasswort (Salicornia europaea) in a polyculture aquaponic system

The aim of this study was to evaluate the effect of starvation and refeeding on the growth and food intake of gilthead seabream (Sparus aurata) and seabass (Dicentrarchus labrax) and on the growth and nitrogen uptake of glasswort (Salicornia europaea) in a polyculture aquaponic system under 12 ppt salinity for 75 days. Nine small-scale autonomous aquaponic systems were used, each containing 10 gilthead seabreams (average weight of 6.33 ± 0.73 g and average length of 5.73 ± 0.72 cm) and 10 seabasses (5.82 ± 0.77 g and 6.35 ± 0.45 cm), as well as five glasswort plants. Three fish feeding treatments were performed, a control (A), in which fish were fed daily until satiation, and two fasting treatments for 4 (B) and 7 days (C). Fish growth performance was significantly lower (p < 0.05) in the C treatment for both species compared to treatments A and B. Food consumption (FC) and feed conversion ratio (FCR) were significantly higher (p < 0.05) in treatment C. Glasswort growth performance was significantly higher in treatment C (p < 0.05). The results showed that the 4-day food-deprived fish were similar to the control fish by achieving partial compensatory growth. The more extended fasting period (7 days) resulted in significantly lower growth performance. The lipid and nitrogen retention levels in both species were significantly lower in food-deprived fish than in the control fish both before and during compensatory growth. The results suggest that a feeding schedule involving starvation-refeeding cycles is a promising feed management option for these species in polyculture aquaponic systems. The effect of food deprivation was also significantly beneficial (p < 0.05) for the growth performance of glasswort compared to the control treatment.

Halophytes as new model plant species for salt tolerance strategies

Soil salinity is becoming a growing issue nowadays, severely affecting the world's most productive agricultural landscapes. With intersecting and competitive challenges of shrinking agricultural lands and increasing demand for food, there is an emerging need to build resilience for adaptation to anticipated climate change and land degradation. This necessitates the deep decoding of a gene pool of crop plant wild relatives which can be accomplished through salt-tolerant species, such as halophytes, in order to reveal the underlying regulatory mechanisms. Halophytes are generally defined as plants able to survive and complete their life cycle in highly saline environments of at least 200-500 mM of salt solution. The primary criterion for identifying salt-tolerant grasses (STGs) includes the presence of salt glands on the leaf surface and the Na⁺ exclusion mechanism since the interaction and replacement of Na⁺ and K⁺ greatly determines the survivability of STGs in saline environments. During the last decades or so, various salt-tolerant grasses/halophytes have been explored for the mining of salt-tolerant genes and testing their efficacy to improve the limit of salt tolerance in crop plants. Still, the utility of halophytes is limited due to the non-availability of any model halophytic plant system as well as the lack of complete genomic information. To date, although Arabidopsis (Arabidopsis thaliana) and salt cress (Thellungiella halophila) are being used as model plants in most salt tolerance studies, these plants are short-lived and can tolerate salinity for a shorter duration only. Thus, identifying the unique genes for salt tolerance pathways in halophytes and their introgression in a related cereal genome for better tolerance to salinity is the need of the hour. Modern technologies including RNA sequencing and genome-wide mapping along with advanced bioinformatics programs have advanced the decoding of the whole genetic information of plants and the development of probable algorithms to correlate stress tolerance limit and yield potential. Hence, this article has been compiled to explore the naturally occurring halophytes as potential model plant species for abiotic stress tolerance and to further breed crop plants to enhance salt tolerance through genomic and molecular tools.

Cold acclimation alleviates cold stress-induced PSII inhibition and oxidative damage in tobacco leaves

This study aimed to explore how cold acclimation (CA) modulates cold stress in tobacco leaves and reveal the relationship between CA and cold stress resistance, and the mechanism of CA-induced plant resistance to cold stress. This study examined the effects of CA treatment (at 8-10℃ for 2 d) on the cold tolerance of tobacco leaves under 4°C cold stress treatment using seedlings without CA treatment as the control (NA). In both CA and NA leaves, cold stress treatment resulted in a decrease in maximum photochemical efficiency of PSII (Fv/Fm), increase in relative variable fluorescence (VJ) at 2 ms on the standardized OJIP curve, inhibition of PSII activity, and impairment of electron transfer on the acceptor side. Besides increasing the malondialdehyde (MDA) content and electrolyte leakage rate, the cold stress exacerbated the degree of membrane peroxidation. The CA treatment also induced the accumulation of reactive oxygen species (ROS), including superoxide anion (O2·-) and H2O2, and increased the activities of antioxidant enzymes, such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbic acid peroxidase (APX). The CA treatment also enhanced the accumulation of soluble sugar (SS) and soluble protein (SP), cyclic electron flow (CEF), and the proportion of regulatory energy dissipation Y(NPQ). Moreover, CA+ cold stress treatment significantly reduced CEF and Y(NPQ) in tobacco leaves than under NA+ cold stress treatment, thus significantly alleviating the degree of PSII photoinhibition. In conclusion, CA treatment significantly alleviated PSII photoinhibition and oxidative damage in tobacco leaves under cold stress treatment. Improvement in cold resistance of tobacco leaves is associated with the induction of antioxidant enzyme activity, accumulation of osmoregulation substances, and initiation of photoprotective mechanisms.

Transcriptome Analysis Reveals Molecular Mechanisms under Salt Stress in Leaves of Foxtail Millet (Setaria italica L.)

Foxtail millet (Setaria italica L.) is an important cereal for managing future water scarcity and ensuring food security, due to its strong drought and salt stress resistance owing to its developed root system. However, the molecular responses of foxtail millet leaves to salt stress are largely unknown. In this study, seeds of 104 foxtail millet accessions were subjected to 0.17 mol·L^-1 NaCl stress during germination, and various germination-related parameters were analyzed to derive 5 salt-sensitive accessions and 13 salt-tolerant accessions. Hong Gu 2000 and Pu Huang Yu were the most salt-tolerant and salt-sensitive accessions, respectively. To determine the mechanism of the salt stress response, transcriptomic differences between the control and salt-treated groups were investigated. We obtained 2019 and 736 differentially expressed genes under salt stress in the salt-sensitive and salt-tolerant accessions, respectively. The transcription factor families bHLH, WRKY, AP2/ERF, and MYB-MYC were found to play critical roles in foxtail millet's response to salt stress. Additionally, the down-regulation of ribosomal protein-related genes causes stunted growth in the salt-sensitive accessions. The salt-tolerant accession alleviates salt stress by increasing energy production. Our findings provide novel insights into the molecular mechanism of foxtail millet's response to salt stress.

Integrated Analysis of Hi-C and RNA-Seq Reveals the Molecular Mechanism of Autopolyploid Growth Advantages in Pak Choi (Brassica rapa ssp. chinensis)

Polyploids generated by the replication of a single genome (autopolyploid) or synthesis of two or more distinct genomes (allopolyploid) usually show significant advantages over their diploid progenitors in biological characteristics, including growth and development, nutrient accumulation, and plant resistance. Whereas, the impacts of genomic replication on transcription regulation and chromatin structure in pak choi have not been explored fully. In this study, we observed the transcriptional and genomic structural alterations between diploid B. rapa (AA) and artificial autotetraploid B. rapa (AAAA) using RNA-seq and Hi-C. RNA-seq revealed 1,786 differentially expressed genes (DEGs) between the diploids and autotetraploids, including 717 down-regulated and 1,069 up-regulated genes in autotetraploids. Of all the 1,786 DEGs, 23 DEGs (10 down-regulated DEGs in autotetraploids) were involved in Compartment A-B shifts, while 28 DEGs (20 up-regulated DEGs in autotetraploids) participated in Compartment B-A shifts. Moreover, there were 15 DEGs in activated topologically associating domains (TADs) (9 up-regulated DEGs in diploids) and 80 DEGs in repressed TADs (49 down-regulated DEGs in diploids). Subsequently, eight DEGs with genomic structural variants were selected as potential candidate genes, including four DEGs involved in photosynthesis (BraA01003143, BraA09002798, BraA04002224, and BraA08000594), three DEGs related to chloroplast (BraA05002974, BraA05001662, and BraA04001148), and one DEG associated with disease resistance (BraA09004451), which all showed high expression in autotetraploids. Overall, our results demonstrated that integrative RNA-seq and Hi-C analysis can identify related genes to phenotypic traits and also provided new insights into the molecular mechanism of the growth advantage of polyploids.

Salt stress proteins in plants: An overview

Salinity stress is considered the most devastating abiotic stress for crop productivity. Accumulating different types of soluble proteins has evolved as a vital strategy that plays a central regulatory role in the growth and development of plants subjected to salt stress. In the last two decades, efforts have been undertaken to critically examine the genome structure and functions of the transcriptome in plants subjected to salinity stress. Although genomics and transcriptomics studies indicate physiological and biochemical alterations in plants, it do not reflect changes in the amount and type of proteins corresponding to gene expression at the transcriptome level. In addition, proteins are a more reliable determinant of salt tolerance than simple gene expression as they play major roles in shaping physiological traits in salt-tolerant phenotypes. However, little information is available on salt stress-responsive proteins and their possible modes of action in conferring salinity stress tolerance. In addition, a complete proteome profile under normal or stress conditions has not been established yet for any model plant species. Similarly, a complete set of low abundant and key stress regulatory proteins in plants has not been identified. Furthermore, insufficient information on post-translational modifications in salt stress regulatory proteins is available. Therefore, in recent past, studies focused on exploring changes in protein expression under salt stress, which will complement genomic, transcriptomic, and physiological studies in understanding mechanism of salt tolerance in plants. This review focused on recent studies on proteome profiling in plants subjected to salinity stress, and provide synthesis of updated literature about how salinity regulates various salt stress proteins involved in the plant salt tolerance mechanism. This review also highlights the recent reports on regulation of salt stress proteins using transgenic approaches with enhanced salt stress tolerance in crops.

High Salinity Reduces Plant Growth and Photosynthetic Performance but Enhances Certain Nutritional Quality of C4 Halophyte Portulaca oleracea L. Grown Hydroponically Under LED Lighting

Portulaca oleracea L. (known as purslane) is one of the most nutritious leafy vegetables owing to its high content of antioxidants. In this study, all plants were grown indoors hydroponically with different NaCl salinities. Photosynthetic photo flux density (PPFD) at 200 μmol m^-2 s^-1 (12 h) was provided to all plants by LED with red:blue ratio of 2.2. Thirty days after transplanting, plants grown with100 mM NaCl had the highest productivity and the fastest leaf growth followed by those with 0, 200 and 300 mM NaCl. Grown with 300 mM NaCl, purslane had the lowest specific leaf area due to its highest leaf dry matter content and its lowest water content. All plants had similar values of leaf succulence except for those with 300 mM NaCl. Total chlorophyll and carotenoids contents were significantly higher in plants grown with 0 and 100 mM NaCl than with 200, and 300 mM NaCl. All plants had F_v/F_m ratios close to 0.8. However, electron transport rate and ΔF/F_m' were significantly higher in plants grown with 0 and 100 mM NaCl than with 200 and 300 mM NaCl. CAM-induced purslane with 300 mM NaCl had higher non-photochemical quenching. Maximum net photosynthetic O₂ evolution rate and Cyt b₆f concentration were significantly lower with 300 mM NaCl compared to all other plants while all plants had similar PS II concentration. Proline concentration increased with increasing salinities. All plants had similar levels of total soluble sugars. Plants grown with 0 and 100 mM NaCl had significantly higher concentrations of NO₃ ^-, total reduced nitrogen, total leaf soluble protein, Rubisco protein, total ascorbic acid, and total phenolic compounds than with 200 and 300 mM NaCl. The highest concentrations of K, Ca, and Mg were found in purslane grown under 0 mM NaCl. Statistically, no significant differences in Fe concentrations were observed among all plants. However, salinity seems to increase Fe concentration. In conclusion, it is feasible to grow purslane under 100 mM NaCl as it is the most optimal condition to achieve higher productivity and better quality. However, the production of antioxidants may depend on not only salinity but also other growth conditions.

Integrated physiological and chloroplast proteome analysis of wheat seedling leaves under salt and osmotic stresses

In this study, we performed an integrated physiological and chloroplast proteome analysis of wheat seedling leaves under salt and osmotic stresses by label-free based quantitative proteomic approach. Both salt and osmotic stresses significantly increased the levels of abscisic acid and methyl jasmonate and led to damages of chloroplast ultrastructure. Main parameters of chlorophyll fluorescence and gas exchange showed a significant decline under both stresses. Quantitative proteomic analysis identified 194 and 169 chloroplast-localized differentially accumulated proteins (DAPs) responsive to salt and osmotic stresses, respectively. The abundance of main DAPs involved in light-dependent reaction were increased under salt stress, but decreased in response to osmotic stress. On the contrary, salt stress induced a significant upregulation of the DAPs associated with Calvin cycle, transcription and translation, amino acid metabolism, carbon and nitrogen metabolism, and some of them exhibited a downregulation under osmotic stress. In particular, both treatments significantly upregulated the DAPs involved in plastoglobule development, protein folding and proteolysis, hormone and vitamin synthesis. Finally, we proposed a putative synergistic responsive network of wheat chloroplast proteome under salt and osmotic stresses, aiming to provide new insights into the underlying response and defense mechanisms of wheat chloroplast proteome in response to abiotic stresses. SIGNIFICANCE: Salt and osmotic stresses are the two most common abiotic stresses that severely affect crop growth and productivity. As the main site of photosynthesis of plant cells, the chloroplast also plays important role in plant tolerance to abiotic stress. However, the response of chloroplast proteome to salt and osmotic is still poorly understood by using the traditional two-dimensional electrophoresis (2-DE) method due to a poor resolution of chloroplast protein separation and low throughput identification of differentially accumulated proteins (DAPs). In this study, we employed label-free based quantitative proteomic approach to perform an integrated physiological and large-scale chloroplast proteome analysis of wheat seedling leaves under salt and osmotic stresses, which laid a solid foundation for future studies into the response and defense mechanisms of wheat chloroplast in response to abiotic stresses.

Na2CO3-responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics

Alkali-salinity exerts severe osmotic, ionic, and high-pH stresses to plants. To understand the alkali-salinity responsive mechanisms underlying photosynthetic modulation and reactive oxygen species (ROS) homeostasis, physiological and diverse quantitative proteomics analyses of alkaligrass (Puccinellia tenuiflora) under Na₂CO₃ stress were conducted. In addition, Western blot, real-time PCR, and transgenic techniques were applied to validate the proteomic results and test the functions of the Na₂CO₃-responsive proteins. A total of 104 and 102 Na₂CO₃-responsive proteins were identified in leaves and chloroplasts, respectively. In addition, 84 Na₂CO₃-responsive phosphoproteins were identified, including 56 new phosphorylation sites in 56 phosphoproteins from chloroplasts, which are crucial for the regulation of photosynthesis, ion transport, signal transduction, and energy homeostasis. A full-length PtFBA encoding an alkaligrass chloroplastic fructose-bisphosphate aldolase (FBA) was overexpressed in wild-type cells of cyanobacterium Synechocystis sp. Strain PCC 6803, leading to enhanced Na₂CO₃ tolerance. All these results indicate that thermal dissipation, state transition, cyclic electron transport, photorespiration, repair of photosystem (PS) II, PSI activity, and ROS homeostasis were altered in response to Na₂CO₃ stress, which help to improve our understanding of the Na₂CO₃-responsive mechanisms in halophytes.

Carbon metabolic rates and GHG emissions in different wetland types of the Ebro Delta

Deltaic wetlands are highly productive ecosystems, which characteristically can act as C-sinks. However, they are among the most threatened ecosystems, being very vulnerable to global change, and require special attention towards its conservation. Knowing their climate change mitigating potential, conservation measures should also be oriented with a climatic approach, to strengthen their regulatory services. In this work we studied the carbon biogeochemistry and the specific relevance of certain microbial guilds on carbon metabolisms of the three main types of deltaic wetlands located in the Ebro Delta, north-eastern Spain, as well as how they deal with human pressures and climate change effects. We estimated the metabolic rates of the main carbon-related metabolisms (primary production and respiration) and the resulting carbon and global warming potential balances in sites with a different salinity range and trophic status. With the results obtained, we tried to define the influence of possible changes in salinity and trophic level linked to the main impacts currently threatening deltaic wetlands, on the C-metabolisms and GHG emissions, for a better understanding of the mitigating capacity and their possible enhancement when applying specific management actions. Metabolic rates showed a pattern highly influenced by the salinity range and nutrients inputs. Freshwater and brackish wetlands, with higher nutrient inputs from agricultural runoff, showed higher C-capture capacity (around 220–250 g C m^-2 y^-1), but also higher rates of degradative metabolisms (aerobic respiration and CH₄ emissions). Contrastingly, the rates of C-related metabolisms and C-retention of Salicornia-type coastal salt marshes were lower (42 g C m^-2 y^-1). The study of the microbial metacommunity composition by the16S RNA gene sequencing revealed a significant higher presence of methanogens in the salt marsh, and also higher metabolic potential, where there was significantly more organic matter content in sediment. Salinity inhibition, however, explained the lower respiration rates, both aerobic and anaerobic, and prevented higher rates of methanogenesis despite the major presence of methanogens. Conservation measures for these wetlands would require, overall, maintaining the sediment contributions of the river basin intending to overcome the regression of the Delta and its salt marshes in a climate change scenario. Particularly, for reducing degradative metabolisms, and favour C-retention, nutrient inputs should be controlled in freshwater and brackish wetlands in order to reduce eutrophication. In salt marshes, the reduction of salinity should be avoided to control increases in methanogenesis and CH₄ emissions.

Physiological and proteomic responses of reactive oxygen species metabolism and antioxidant machinery in mulberry (Morus alba L.) seedling leaves to NaCl and NaHCO3 stress

In this paper, the effects of 100 mM NaCl and NaHCO₃ stress on reactive oxygen species (ROS) and physiological and proteomic aspects of ROS metabolism in mulberry seedling leaves were studied. The results showed that NaCl stress had little effect on photosynthesis and respiration of mulberry seedling leaves. Superoxide dismutase (SOD) activity and the expression of related proteins in leaves increased by varying degrees, and accumulation of superoxide anion (O₂·^-) not observed. Under NaHCO₃ stress, photosynthesis and respiration were significantly inhibited, while the rate of O₂·^- production rate and H₂O₂ content increased. The activity of catalase (CAT) and the expression of CAT (W9RJ43) increased under NaCl stress. In response to NaHCO₃ stress, the activity and expression of CAT were significantly decreased, but the ability of H₂O₂ scavenging of peroxidase (POD) was enhanced. The ascorbic acid-glutathione (AsA-GSH) cycle in mulberry seedling leaves was enhancement in both NaCl and NaHCO₃ stress. The expression of 2-Cys peroxiredoxin BAS1 (2-Cys Prx BAS1), together with thioredoxin F (TrxF), thioredoxin O1 (TrxO1), thioredoxin-like protein CITRX (Trx CITRX), and thioredoxin-like protein CDSP32 (Trx CDSP32) were significantly increased under NaCl stress. Under NaHCO₃ stress, the expression of the electron donor of ferredoxin-thioredoxin reductase (FTR), together with Trx-related proteins, such as thioredoxin M (TrxM), thioredoxin M4 (TrxM4), thioredoxin X (TrxX), TrxF, and Trx CSDP32 were significantly decreased, suggesting that the thioredoxin-peroxiredoxin (Trx-Prx) pathway's function of scavenging H₂O₂ of in mulberry seedling leaves was inhibited. Taken together, under NaCl stress, excessive production of O₂·^- mulberry seedlings leaves was inhibited, and H₂O₂ was effectively scavenged by CAT, AsA-GSH cycle and Trx-Prx pathway. Under NaHCO₃ stress, despite the enhanced functions of POD and AsA-GSH cycle, the scavenging of O₂·^- by SOD was not effective, and that of H₂O₂ by CAT and Trx-Prx pathway were inhibited; and in turn, the oxidative damage to mulberry seedling leaves could not be reduced.

Transcriptome Analysis of ppdnmt2 and Identification of Superoxide Dismutase as a Novel Interactor of DNMT2 in the Moss Physcomitrella patens

DNMT2 is a DNA/tRNA cytosine methyltransferase that is highly conserved in structure and function in eukaryotes. In plants however, limited information is available on the function of this methyltransferase. We have previously reported that in the moss Physcomitrella patens, DNMT2 plays a crucial role in stress recovery and tRNA^Asp transcription/stability under salt stress. To further investigate the role of PpDNMT2 at genome level, in this study we have performed RNA sequencing of ppdnmt2. Transcriptome analysis reveals a number of genes and pathways to function differentially and suggests a close link between PpDNMT2 function and osmotic and ionic stress tolerance. We propose PpDNMT2 to play a pivotal role in regulating salt tolerance by affecting molecular networks involved in stress perception and signal transduction that underlie maintenance of ion homeostasis in cells. We also examined interactome of PpDNMT2 using affinity purification (AP) coupled to mass spectrometry (AP-MS). Quantitative proteomic analysis reveals several chloroplast proteins involved in light reactions and carbon assimilation and proteins involved in stress response and some not implicated in stress to co-immunoprecipitate with PpDNMT2. Comparison between transcriptome and interactome datasets has revealed novel association between PpDNMT2 activity and the antioxidant enzyme Superoxide dismutase (SOD), protein turnover mediated by the Ubiquitin-proteasome system and epigenetic gene regulation. PpDNMT2 possibly exists in complex with CuZn-SODs in vivo and the two proteins also directly interact in the yeast nucleus as observed by yeast two-hybrid assay. Taken together, the work presented in this study sheds light on diverse roles of PpDNMT2 in maintaining molecular and physiological homeostasis in P. patens. This is a first report describing transcriptome and interactome of DNMT2 in any land plant.

Physiological and Proteomic Analyses Reveal Adaptive Mechanisms of Ryegrass (Annual vs. Perennial) Seedlings to Salt Stress

Ryegrass has a relatively high salt tolerance and is considered to be a promising species for both foraging and turf purposes in salt-affected soils in China. While annual ryegrass and perennial ryegrass are two different species, they have similar genomes. However, little is known about their physiological and molecular response mechanisms to salinity stress. Here, biomass, chlorophyll fluorescence, and inorganic ion and organic solute content were measured. 2-DE-based proteomic technology was then used to identify the differentially expressed proteins in the salt-treated seedlings. The results showed that salt stress reduced growth and photosynthesis in the seedlings of both species, but much more so in annual ryegrass. With increasing salinity, the Na+ concentration increased while the K+ concentration decreased in both species, and the sugars and proline increased as the primary organic solutes used to cope with osmotic stress. Additionally, proteomic analysis revealed 33 and 37 differentially expressed proteins in annual and perennial ryegrass, respectively. Most of the identified proteins were involved in carbohydrate and energy metabolism, photosynthesis, genetic information processes, amino acid metabolism, stress defense, and protein synthesis and folding. The results suggest that the two-ryegrass species had different physiological and proteomic responses. These findings can provide new insights into physiological mechanisms by which ryegrass species respond to salt stress.

Transcriptome profiling and environmental linkage to salinity across Salicornia europaea vegetation

BACKGROUND

Salicornia europaea, a succulent obligatory halophyte is the most salt-tolerant plant species in the world. It survives salt concentrations of more than 1 M. Therefore, it is a suitable model plant to identify genes involved in salt tolerance mechanisms that can be used for the improvement of crops. The changes in a plant's gene expression in response to abiotic stresses may depend on factors like soil conditions at the site, seasonality, etc. To date, experiments were performed to study the gene expression of S. europaea only under controlled conditions. Conversely, the present study investigates the transcriptome and physicochemical parameters of S. europaea shoots and roots from two different types of saline ecosystems growing under natural conditions.

RESULTS

The level of soil salinity was higher at the naturally saline site than at the anthropogenic saline site. The parameters such as EC_e, Na⁺, Cl^-, Ca⁺, SO₄^2- and HCO₃^- of the soils and plant organs significantly varied according to sites and seasons. We found that Na⁺ mainly accumulated in shoots, whereas K⁺ and Ca²⁺ levels were higher in roots throughout the growing period. Moreover, changes in S. europaea gene expression were more prominent in seasons, than sites and plant organs. The 30 differentially expressed genes included enzymes for synthesis of S-adenosyl methionine, CP47 of light-harvesting complex II, photosystem I proteins, Hsp70 gene, ATP-dependent Clp proteases, ribulose bisphosphate carboxylase/oxygenase (Rubisco), phenylalanine ammonia-lyase (PAL), cytochrome c oxidase (COX) and ATP synthase.

CONCLUSION

The comparisons made based on two seasons, plant organs and two different sites suggest the importance of seasonal variations in gene expression of S. europaea. We identify the genes that may play an important role in acclimation to season-dependent changes of salinity. The genes were involved in processes such as osmotic adjustment, energy metabolism and photosynthesis.

Comparative physiological and proteomic analyses of the chloroplasts in halophyte Sesuvium portulacastrum under differential salt conditions

Sesuvium portulacastrum, an important mangrove-associated true halophyte belongs to the family Aizoaceae, has excellent salt tolerance. Chloroplasts are the most sensitive organelles involved in the response to salinity. However, the regulation mechanism of chloroplasts of S. portulacastrum under salinity stress has not been reported. In this study, morphological and physiological analyses of leaves and comparative proteomics of chloroplasts isolated from the leaves of S. portulacastrum under different NaCl treatments were performed. Our results showed that the thickness of the palisade tissue, the leaf area, the maximum photochemical efficiency of photosystem II, and the electron transport rate increased remarkably after the plants were subjected to differential saline environments, indicating that salinity can increase photosynthetic efficiency and improve the growth of S. portulacastrum. Subsequently, 55 differentially expressed protein species (DEPs) from the chloroplasts of S. portulacastrum under differential salt conditions were positively identified by mass spectrometry. These DEPs were involved in multiple metabolic pathways, such as photosynthesis, carbon metabolism, ATP synthesis and the cell structure. Among these DEPs, the abundance of most proteins was induced by salt stress. Based on a combination of the morphological and physiological data, as well as the chloroplast proteome results, we speculated that S. portulacastrum can maintain photosynthetic efficiency and growth by maintaining the stability of the photosystem II complex, promoting the photochemical reaction rate, enhancing carbon fixation, developing plastoglobules, and preserving the biomembrane system of chloroplasts under salt stress.

Study of the beneficial effects of green light on lettuce grown under short-term continuous red and blue light-emitting diodes

Red and blue light are the most important light spectra for driving photosynthesis to produce adequate crop yield. It is also believed that green light may contribute to adaptations to growth. However, the effects of green light, which can trigger specific and necessary responses of plant growth, have been underestimated in the past. In this study, lettuce (Lactuca sativa L.) was exposed to different continuous light (CL) conditions for 48 h by a combination of red and blue light-emitting diodes (LEDs) supplemented with or without green LEDs, in an environmental-controlled growth chamber. Green light supplementation enhanced photosynthetic capacity by increasing net photosynthetic rates, maximal photochemical efficiency, electron transport for carbon fixation (JPSII ) and chlorophyll content in plants under the CL treatment. Green light decreased malondialdehyde and H2 O2 accumulation by increasing the activities of superoxide dismutase (EC 1.15.1.1) and ascorbate peroxidase (EC 1.11.1.11) after 24 h of CL. Supplemental green light significantly increased the expression of photosynthetic genes LHCb and PsbA from 6 to 12 h, and these gene expressions were maintained at higher levels than those under other light conditions between 12 and 24 h. However, a notable downregulation of both LHCb and PsbA was observed during 24 to 48 h. These results indicate that the effects of green light on lettuce plant growth, via enhancing activity of particular components of antioxidative enzyme system and promoting of LHCb and PsbA expression to maintain higher photosynthetic capacity, alleviated a number of the negative effects caused by CL.

Bacterial microbiome of root-associated endophytes of Salicornia europaea in correspondence to different levels of salinity

The halophytes have evolved several strategies to survive in saline environments; however, an additional support from their associated microbiota helps combat adverse conditions. Hence, our driving interests to investigate the endophytic bacterial community richness, diversity, and composition associated to roots of Salicornia europaea from two test sites with different origins of soil salinity. We assumed that salinity will have a negative effect on the diversity of endophytes but simultaneously will permit the high occurrence of halophylic bacteria. Further, to establish the role of the host and its external environment in determining the endophytic diversity, we analyzed the physico-chemical parameters of root zone soil and the concentration of salt ions in the plant roots. The results based on the Miseq Illumina sequencing approach revealed a higher number of endophytic bacterial OTUs at naturally saline test site with a higher level of soil salinity. Proteobacteria and Bacteriodetes were the dominant endophytic phyla at both analyzed sites; additionally, the high occurrence of Planctomycetes and Acidobacteria at more saline site and the occurrence of Firmicutes, Actinobacteria, and Chloroflexi at less saline site were recorded. The salinity in the root zone soil was crucial in structuring the endophytic community of S. europaea, and the significant prevalence of representatives from the phyla Deltaproteobacteria, Acidobacteria, Caldithrix, Fibrobacteres, and Verrucomicrobia at the more saline test site suggest domination of halophylic bacteria with potential role in mitigation of salt stress of halophytes.

Relative contribution of Na+/K+ homeostasis, photochemical efficiency and antioxidant defense system to differential salt tolerance in cotton (Gossypium hirsutum L.) cultivars

In this study, the role of specific components of different coping strategies to salt load were identified. A pot experiment was conducted with four cotton (Gossypium hirsutum L.) cultivars (differing in salt-sensitivity) under salinity stress. Based on observed responses in growth performance and physiological characteristics, CZ91 was the most tolerant of the four cultivars, followed by cultivars CCRI44 and CCRI49, with Z571 being much more sensitive to salt stress. To perform this tolerant response, they implement different adaptative mechanisms to cope with salt-stress. The superior salt tolerance of CZ91 was conferred by at least three complementary physiological mechanisms: its ability to regulate K⁺ and Na⁺ transport more effectively, its higher photochemical efficiency and better antioxidant defense capacity. However, only one or a few specific components of these defense systems play crucial roles in moderately salt tolerant CCRI44 and CCRI49. Lower ROS load in CCRI44 may be attributed to simultaneous induction of antioxidant defenses by maintaining an unusually high level of SOD, and higher activities of CAT, APX, and POD during salt stress. CCRI49 could reduce the excess generation of ROS not only by maintaining a higher selective absorption of K⁺ over Na⁺ in roots across the membranes through SOS1, AKT1, and HAK5, but also by displaying higher excess-energy dissipation (e.g., higher ETR, P_R and qN) during salt stress. Overall, our data provide a mechanistic explanation for differential salt stress tolerance among these cultivars and shed light on the different strategies employed by cotton cultivars to minimize the ill effects of stress.

Establishment of a gene function analysis system for the euhalophyte Salicornia europaea L

A Salicornia europaea L. in vitro cell transformation system was developed and further applied to SeNHX1 function investigation. The exploration of salt-tolerant genes from halophyte has seriously been limited by the lack of self-dependent transformation system. Here, an Agrobacterium tumefaciens-mediated in vitro cell transformation system of euhalophyte Salicornia europaea L. was developed. Calli derived from hypocotyl of S. europaea were co-cultured for 3 days with Agrobacterium at OD₆₀₀ ranging from 1.0 to 1.5 and then selected with 25 mg/L hygromycin (Hyg). The transformed cells were identified from Hyg positive calli by GUS assay and qRT-PCR, and the transformation efficiency was up to 74.4%. The practicality of this system was further tested via genetic manipulation of S. europaea Na⁺/H⁺ antiporter 1 (SeNHX1) gene by creating the overexpressing, silencing, and empty vector cells. Survival ratio and Na⁺ distribution under salt treatment showed obvious differences in SeNHX1-overexpressing, -silencing, and empty vector cells, indicating the feasibility of this system to analyze gene function. This investigation is enlightening for studies in other non-model plants lacking of self-dependent transformation system.

Incorporating thresholds into understanding salinity tolerance: A study using salt-tolerant plants in salt marshes

Although salinity in many ecosystems such as salt marshes can be extremely high, an asymmetry in salinity range between experimental studies (relatively narrow) and field conditions (potentially broad) has strongly affected current understanding of plant salinity tolerance. To improve understanding, it is thus important to examine plant tolerances over a broad range of salinities and identify potential tolerance thresholds. We examine tolerances of two widely distributed marsh plants, Suaeda salsa and Salicornia europaea, to salinities ranging from 0 to 100 g/kg, and determine survival, above‐ and belowground biomass after 8 weeks of salinity treatment. Both species, Sa. europaea in particular, have much broader salinity tolerances than other plants previously examined, (2) plant survival, above‐ and belowground biomass have remarkably different responses to salinity, and (3) there is a nonlinear, threshold response of S. salsa to salinity, above which S. salsa survivorship drastically decreases. These results provide multiple important insights. Our study suggests that the potential for using these halophytes to revegetate and restore salt‐affected land may be greater than previously thought, and highlights the importance of studying multiple plant responses. Importantly, our study calls for a better integration of thresholds into understanding plant salinity tolerances and their applications.

Salinity Response in Chloroplasts: Insights from Gene Characterization

Salinity is a severe abiotic stress limiting agricultural yield and productivity. Plants have evolved various strategies to cope with salt stress. Chloroplasts are important photosynthesis organelles, which are sensitive to salinity. An understanding of molecular mechanisms in chloroplast tolerance to salinity is of great importance for genetic modification and plant breeding. Previous studies have characterized more than 53 salt-responsive genes encoding important chloroplast-localized proteins, which imply multiple vital pathways in chloroplasts in response to salt stress, such as thylakoid membrane organization, the modulation of photosystem II (PS II) activity, carbon dioxide (CO₂) assimilation, photorespiration, reactive oxygen species (ROS) scavenging, osmotic and ion homeostasis, abscisic acid (ABA) biosynthesis and signaling, and gene expression regulation, as well as protein synthesis and turnover. This review presents an overview of salt response in chloroplasts revealed by gene characterization efforts.

Stoichiometric variation of halophytes in response to changes in soil salinity

Variation in soil salt may change the stoichiometry of a halophyte by altering plant ecophysiology, and exert different influences on various plant organs, which has potentially important consequences for the nutrition of consumers as well as nutrient cycling in a saline ecosystem. Using a greenhouse pot experiment, we investigated the effect of salinity variability on the growth and stoichiometry of different organs of Suaeda glauca and Salicornia europaea - two dominant species of important ecological and economic value in the saline ecosystem. Our results showed that appropriate salt stimulated the growth of both species during the vigorous growth period, while high salt suppressed growth. Na significantly increased with increased salt in the culture, whereas concentrations of other measured elements and K:Na ratio for both species significantly decreased at low salt treatments, and became more gradual under higher salt conditions. Furthermore, with the change of salt in culture, variations in leaf (degenerated leaf for S. europaea, considered as young stem) stoichiometry, except N:P ratio, were large and less in stems (old stems for S. europaea) than in roots, reflecting physiological and biochemical reactions in the leaf in response to salt stress, supported by sharp changes in trends. These results suggest that appropriate saline conditions can enhance biological C fixation of halophytes; however, increasing salt could affect consumer health and decrease cycling of other nutrients in saline ecosystems.

iTRAQ-Based Quantitative Proteomic Analysis of Spirulina platensis in Response to Low Temperature Stress

Low temperature (LT) is one of the most important abiotic stresses that can significantly reduce crop yield. To gain insight into how Spirulina responds to LT stress, comprehensive physiological and proteomic analyses were conducted in this study. Significant decreases in growth and pigment levels as well as excessive accumulation of compatible osmolytes were observed in response to LT stress. An isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomics approach was used to identify changes in protein abundance in Spirulina under LT. A total of 3,782 proteins were identified, of which 1,062 showed differential expression. Bioinformatics analysis indicated that differentially expressed proteins that were enriched in photosynthesis, carbohydrate metabolism, amino acid biosynthesis, and translation are important for the maintenance of cellular homeostasis and metabolic balance in Spirulina when subjected to LT stress. The up-regulation of proteins involved in gluconeogenesis, starch and sucrose metabolism, and amino acid biosynthesis served as coping mechanisms of Spirulina in response to LT stress. Moreover, the down-regulated expression of proteins involved in glycolysis, TCA cycle, pentose phosphate pathway, photosynthesis, and translation were associated with reduced energy consumption. The findings of the present study allow a better understanding of the response of Spirulina to LT stress and may facilitate in the elucidation of mechanisms underlying LT tolerance.

Salt-stress-responsive chloroplast proteins in Brassica juncea genotypes with contrasting salt tolerance and their quantitative PCR analysis

Brassica juncea is mainly cultivated in the arid and semi-arid regions of India where its production is significantly affected by soil salinity. Adequate knowledge of the mechanisms underlying the salt tolerance at sub-cellular levels must aid in developing the salt-tolerant plants. A proper functioning of chloroplasts under salinity conditions is highly desirable to maintain crop productivity. The adaptive molecular mechanisms offered by plants at the chloroplast level to cope with salinity stress must be a prime target in developing the salt-tolerant plants. In the present study, we have analyzed differential expression of chloroplast proteins in two Brassica juncea genotypes, Pusa Agrani (salt-sensitive) and CS-54 (salt-tolerant), under the effect of sodium chloride. The chloroplast proteins were isolated and resolved using 2DE, which facilitated identification and quantification of 12 proteins that differed in expression in the salt-tolerant and salt-sensitive genotypes. The identified proteins were related to a variety of chloroplast-associated molecular processes, including oxygen-evolving process, PS I and PS II functioning, Calvin cycle and redox homeostasis. Expression analysis of genes encoding differentially expressed proteins through real time PCR supported our findings with proteomic analysis. The study indicates that modulating the expression of chloroplast proteins associated with stabilization of photosystems and oxidative defence plays imperative roles in adaptation to salt stress.

Proteomic responses in shoots of the facultative halophyte Aeluropus littoralis (Poaceae) under NaCl salt stress

Salinity is an environmental constraint that limits agricultural productivity worldwide. Studies on the halophytes provide valuable information to describe the physiological and molecular mechanisms of salinity tolerance. Therefore, because of genetic relationships of Aeluropus littoralis (Willd) Parl. with rice, wheat and barley, the present study was conducted to investigate changes in shoot proteome patterns in response to different salt treatments using proteomic methods. To examine the effect of salinity on A. littoralis proteome pattern, salt treatments (0, 200 and 400mM NaCl) were applied for 24h and 7 and 30 days. After 24h and 7 days exposure to salt treatments, seedlings were fresh and green, but after 30 days, severe chlorosis was established in old leaves of 400mM NaCl-salt treated plants. Comparative proteomic analysis of the leaves revealed that the relative abundance of 95 and 120 proteins was significantly altered in 200 and 400mM NaCl treated plants respectively. Mass spectrometry-based identification was successful for 66 out of 98 selected protein spots. These proteins were mainly involved in carbohydrate, energy, amino acids and protein metabolisms, photosynthesis, detoxification, oxidative stress, translation, transcription and signal transduction. These results suggest that the reduction of proteins related to photosynthesis and induction of proteins involved in glycolysis, tricarboxylic acid (TCA) cycle, and energy metabolism could be the main mechanisms for salt tolerance in A. littoralis. This study provides important information about salt tolerance, and a framework for further functional studies on the identified proteins in A. littoralis.

Comparative Proteomic and Physiological Analysis Reveals the Variation Mechanisms of Leaf Coloration and Carbon Fixation in a Xantha Mutant of Ginkgo biloba L

Yellow-green leaf mutants are common in higher plants, and these non-lethal chlorophyll-deficient mutants are ideal materials for research on photosynthesis and plant development. A novel xantha mutant of Ginkgo biloba displaying yellow-colour leaves (YL) and green-colour leaves (GL) was identified in this study. The chlorophyll content of YL was remarkably lower than that in GL. The chloroplast ultrastructure revealed that YL had less dense thylakoid lamellae, a looser structure and fewer starch grains than GL. Analysis of the photosynthetic characteristics revealed that YL had decreased photosynthetic activity with significantly high nonphotochemical quenching. To explain these phenomena, we analysed the proteomic differences in leaves and chloroplasts between YL and GL of ginkgo using two-dimensional gel electrophoresis (2-DE) coupled with MALDI-TOF/TOF MS. In total, 89 differential proteins were successfully identified, 82 of which were assigned functions in nine metabolic pathways and cellular processes. Among them, proteins involved in photosynthesis, carbon fixation in photosynthetic organisms, carbohydrate/energy metabolism, amino acid metabolism, and protein metabolism were greatly enriched, indicating a good correlation between differentially accumulated proteins and physiological changes in leaves. The identifications of these differentially accumulated proteins indicates the presence of a specific different metabolic network in YL and suggests that YL possess slower chloroplast development, weaker photosynthesis, and a less abundant energy supply than GL. These studies provide insights into the mechanism of molecular regulation of leaf colour variation in YL mutants.

Comparative proteomic analysis reveals the positive effect of exogenous spermidine on photosynthesis and salinity tolerance in cucumber seedlings

Our results based on proteomics data and physiological alterations proposed the putative mechanism of exogenous Spd enhanced salinity tolerance in cucumber seedlings. Current studies showed that exogenous spermidine (Spd) could alleviate harmful effects of salinity. It is important to increase our understanding of the beneficial physiological responses of exogenous Spd treatment, and to determine the molecular responses underlying these responses. Here, we combined a physiological analysis with iTRAQ-based comparative proteomics of cucumber (Cucumis sativus L.) leaves, treated with 0.1 mM exogenous Spd, 75 mM NaCl and/or exogenous Spd. A total of 221 differentially expressed proteins were found and involved in 30 metabolic pathways, such as photosynthesis, carbohydrate metabolism, amino acid metabolism, stress response, signal transduction and antioxidant. Based on functional classification of the differentially expressed proteins and the physiological responses, we found cucumber seedlings treated with Spd under salt stress had higher photosynthesis efficiency, upregulated tetrapyrrole synthesis, stronger ROS scavenging ability and more protein biosynthesis activity than NaCl treatment, suggesting that these pathways may promote salt tolerance under high salinity. This study provided insights into how exogenous Spd protects photosynthesis and enhances salt tolerance in cucumber seedlings.

Halophytes as a source of salt tolerance genes and mechanisms: a case study for the Salt Lake area, Turkey

The worst case scenario of global climate change predicts both drought and salinity would be the first environmental factors restricting agriculture and natural ecosystems, causing decreased crop yields and plant growth that would directly affect human population in the next decades. Therefore, it is vital to understand the biology of plants that are already adapted to these extreme conditions. In this sense, extremophiles such as the halophytes offer valuable genetic information for understanding plant salinity tolerance and to improve the stress tolerance of crop plants. Turkey has ecological importance for its rich biodiversity with up to 3700 endemic plants. Salt Lake (Lake Tuz) in Central Anatolia, one of the largest hypersaline lakes in the world, is surrounded by salty marshes, with one of the most diverse floras in Turkey, where arid and semiarid areas have increased due to low rainfall and high evaporation during the summer season. Consequently, the Salt Lake region has a large number of halophytic, xerophytic and xero-halophytic plants. One good example is Eutrema parvulum (Schrenk) Al-Shehbaz & Warwick, which originates from the Salt Lake region, can tolerate up to 600mM NaCl. In recent years, the full genome of E. parvulum was published and it has been accepted as a model halophyte due to its close relationship (sequence identity in range of 90%) with Arabidopsis thaliana (L. Heynh.). In this context, this review will focus on tolerance mechanisms involving hormone signalling, accumulation of compatible solutes, ion transporters, antioxidant defence systems, reactive oxygen species (ROS) signalling mechanism of some lesser-known extremophiles growing in the Salt Lake region. In addition, current progress on studies conducted with E. parvulum will be evaluated to shed a light on future prospects for improved crop tolerance.

Proteomics, photosynthesis and salt resistance in crops: An integrative view

Salinity is a stressful condition that causes a significant decrease in crop production worldwide. Salt stress affects several photosynthetic reactions, including the modulation of several important proteins. Despite these effects, few molecular-biochemical markers have been identified and evaluated for their importance in improving plant salt resistance. Proteomics is a powerful tool that allows the analysis of multigenic events at the post-translational level that has been widely used to evaluate protein modulation changes in plants exposed to salt stress. However, these studies are frequently fragmented and the results regarding photosynthesis proteins in response to salinity are limited. These constraints could be related to the low number of important photosynthetic proteins differently modulated in response to salinity, as has been commonly revealed by conventional proteomics. In this review, we present an evaluation and perspective on the integrated application of proteomics for the identification of photosynthesis proteins to improve salt resistance. We propose the use of phospho-, thiol- and redox-proteomics, associated with the utilization of isolated chloroplasts or photosynthetic sub-organellar components. This strategy may allow the characterization of essential proteins, providing a better understanding of photosynthesis regulation. Furthermore, this may contribute to the selection of molecular markers to improve salt resistance in crops.

Coordinated Changes in Antioxidative Enzymes Protect the Photosynthetic Machinery from Salinity Induced Oxidative Damage and Confer Salt Tolerance in an Extreme Halophyte Salvadora persica L

Salinity-induced modulations in growth, photosynthetic pigments, relative water content (RWC), lipid peroxidation, photosynthesis, photosystem II efficiency, and changes in activity of various antioxidative enzymes were studied in the halophyte Salvadora persica treated with various levels of salinity (0, 250, 500, 750, and 1000 mM NaCl) to obtain an insight into the salt tolerance ability of this halophyte. Both fresh and dry biomass as well as leaf area (LA) declined at all levels of salinity whereas salinity caused an increase in leaf succulence. A gradual increase was observed in the Na(+) content of leaf with increasing salt concentration up to 750 mM NaCl, but at higher salt concentration (1000 mM NaCl), the Na(+) content surprisingly dropped down to the level of 250 mM NaCl. The chlorophyll and carotenoid contents of the leaf remained unaffected by salinity. The photosynthetic rate (PN), stomatal conductance (gs), the transpiration rate (E), quantum yield of PSII (ΦPSII), photochemical quenching (qP), and electron transport rate remained unchanged at low salinity (250 to 500 mM NaCl) whereas, significant reduction in these parameters were observed at high salinity (750 to 1000 mM NaCl). The RWC% and water use efficiency (WUE) of leaf remained unaffected by salinity. The salinity had no effect on maximum quantum efficiency of PS II (Fv/Fm) which indicates that PS II is not perturbed by salinity-induced oxidative damage. Analysis of the isoforms of antioxidative enzymes revealed that the leaves of S. persica have two isoforms each of Mn-SOD and Fe-SOD and one isoform of Cu-Zn SOD, three isoforms of POX, two isoforms of APX and one isoform of CAT. There was differential responses in activity and expression of different isoforms of various antioxidative enzymes. The malondialdehyde (MDA) content (a product of lipid peroxidation) of leaf remained unchanged in S. persica treated with various levels of salinity. Our results suggest that the absence of pigment degradation, the reduction of water loss, and the maintenance of WUE and protection of PSII from salinity-induced oxidative damage by the coordinated changes in antioxidative enzymes are important factors responsible for salt tolerance of S. persica.

Proteomics, metabolomics, and ionomics perspectives of salinity tolerance in halophytes

Halophytes are plants which naturally survive in saline environment. They account for ∼1% of the total flora of the world. They include both dicots and monocots and are distributed mainly in arid, semi-arid inlands and saline wet lands along the tropical and sub-tropical coasts. Salinity tolerance in halophytes depends on a set of ecological and physiological characteristics that allow them to grow and flourish in high saline conditions. The ability of halophytes to tolerate high salt is determined by the effective coordination between various physiological processes, metabolic pathways and protein or gene networks responsible for delivering salinity tolerance. The salinity responsive proteins belong to diverse functional classes such as photosynthesis, redox homeostasis; stress/defense, carbohydrate and energy metabolism, protein metabolism, signal transduction and membrane transport. The important metabolites which are involved in salt tolerance of halophytes are proline and proline analog (4-hydroxy-N-methyl proline), glycine betaine, pinitol, myo-inositol, mannitol, sorbitol, O-methylmucoinositol, and polyamines. In halophytes, the synthesis of specific proteins and osmotically active metabolites control ion and water flux and support scavenging of oxygen radicals under salt stress condition. The present review summarizes the salt tolerance mechanisms of halophytes by elucidating the recent studies that have focused on proteomic, metabolomic, and ionomic aspects of various halophytes in response to salinity. By integrating the information from halophytes and its comparison with glycophytes could give an overview of salt tolerance mechanisms in halophytes, thus laying down the pavement for development of salt tolerant crop plants through genetic modification and effective breeding strategies.

The beta subunit of glyceraldehyde 3-phosphate dehydrogenase is an important factor for maintaining photosynthesis and plant development under salt stress-Based on an integrative analysis of the structural, physiological and proteomic changes in chloroplasts in Thellungiella halophila

Thellungiella halophila, a new model halophyte, can survive under highly saline conditions. We performed comparative proteomics of chloroplasts from plants grown under different saline conditions. Seventy-five salt-responsive proteins were positively identified by mass spectrometry, which represented 43 unique ones. These proteins were categorized into 7 main pathways: light reaction, carbon fixation, energy metabolism, antenna proteins, cell structure, and protein degradation and folding. Saline conditions increased the abundance of proteins involved in photosynthesis, energy metabolism and cell structure. The results indicated that Thellungiella could withstand high salinity by maintaining normal or high photosynthetic capacity, reducing ROS production, as well as enhancing energy usage. Meanwhile, the ultrastructural and physiological data also agree with chloroplast proteomics results. Subsequently, the glyceraldehydes 3-phosphate dehydrogenase beta subunit (GAPB) involved in carbon fixation was selected and its role in salt tolerance was clarified by over-expressing it in Arabidopsis. ThGAPB-overexpressing plants had higher total chlorophyll contents, dry weights, water contents and survival rates than that of wild type plants. These results indicated that ThGAPB might improve plant salt tolerance by maintaining higher recycling rates of ADP and NADP(+) to decrease ROS production, helping to maintain photosynthetic efficiency and plant development under saline conditions.

Physiological and proteomic analyses of salt stress response in the halophyte Halogeton glomeratus

Very little is known about the adaptation mechanism of Chenopodiaceae Halogeton glomeratus, a succulent annual halophyte, under saline conditions. In this study, we investigated the morphological and physiological adaptation mechanisms of seedlings exposed to different concentrations of NaCl treatment for 21 d. Our results revealed that H. glomeratus has a robust ability to tolerate salt; its optimal growth occurs under approximately 100 mm NaCl conditions. Salt crystals were deposited in water-storage tissue under saline conditions. We speculate that osmotic adjustment may be the primary mechanism of salt tolerance in H. glomeratus, which transports toxic ions such as sodium into specific salt-storage cells and compartmentalizes them in large vacuoles to maintain the water content of tissues and the succulence of the leaves. To investigate the molecular response mechanisms to salt stress in H. glomeratus, we conducted a comparative proteomic analysis of seedling leaves that had been exposed to 200 mm NaCl for 24 h, 72 h and 7 d. Forty-nine protein spots, exhibiting significant changes in abundance after stress, were identified using matrix-assisted laser desorption ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF MS/MS) and similarity searches across EST database of H. glomeratus. These stress-responsive proteins were categorized into nine functional groups, such as photosynthesis, carbohydrate and energy metabolism, and stress and defence response.

High-throughput deep sequencing reveals that microRNAs play important roles in salt tolerance of euhalophyte Salicornia europaea

BACKGROUND

microRNAs (miRNAs) are implicated in plant development processes and play pivotal roles in plant adaptation to environmental stresses. Salicornia europaea, a salt mash euhalophyte, is a suitable model plant to study salt adaptation mechanisms. S. europaea is also a vegetable, forage, and oilseed that can be used for saline land reclamation and biofuel precursor production on marginal lands. Despite its importance, no miRNA has been identified from S. europaea thus far.

RESULTS

Deep sequencing was performed to investigate small RNA transcriptome of S. europaea. Two hundred and ten conserved miRNAs comprising 51 families and 31 novel miRNAs (including seven miRNA star sequences) belonging to 30 families were identified. About half (13 out of 31) of the novel miRNAs were only detected in salt-treated samples. The expression of 43 conserved and 13 novel miRNAs significantly changed in response to salinity. In addition, 53 conserved and 13 novel miRNAs were differentially expressed between the shoots and roots. Furthermore, 306 and 195 S. europaea unigenes were predicted to be targets of 41 conserved and 29 novel miRNA families, respectively. These targets encoded a wide range of proteins, and genes involved in transcription regulation constituted the largest category. Four of these genes encoding laccase, F-box family protein, SAC3/GANP family protein, and NADPH cytochrome P-450 reductase were validated using 5'-RACE.

CONCLUSIONS

Our results indicate that specific miRNAs are tightly regulated by salinity in the shoots and/or roots of S. europaea, which may play important roles in salt tolerance of this euhalophyte. The S. europaea salt-responsive miRNAs and miRNAs that target transcription factors, nucleotide binding site-leucine-rich repeat proteins and enzymes involved in lignin biosynthesis as well as carbon and nitrogen metabolism may be applied in genetic engineering of crops with high stress tolerance, and genetic modification of biofuel crops with high biomass and regulatable lignin biosynthesis.

Proteomic analysis of changes in the Kandelia candel chloroplast proteins reveals pathways associated with salt tolerance

The plant chloroplast is one of the most sensitive organelles in response to salt stress. Chloroplast proteins extracted from seedling leaves were separated by two-dimensional gel electrophoresis (2-DE). More than 600 protein spots could be distinguished on each gel. Fifty-eight differentially expressed protein spots were detected, of which 46 could be identified through matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF-MS). These proteins were found to be involved in multiple aspects of chloroplast metabolism pathways such as photosynthesis, ATP synthesis, detoxification and antioxidation processes, nitrogen assimilation and fixation, protein metabolism, and tetrapyrrole biosynthesis. The results indicated that K. candel could withstand up to 500 mM NaCl stress for a measured period of 3 days, by maintaining normal or high photosynthetic electron transfer efficiency and an only slightly stimulated Calvin cycle. Meanwhile, we found that ROS scavenging, nitrogen assimilation, protein degradation and chaperone function in chloroplasts were also of importance for salt tolerance of K. candel. The ultrastructural and physiological data agree with chloroplast proteome results. These findings allow further exploration of our knowledge on salt adaptation in woody halophytes and may contribute to the development of more salt-tolerant plants in the future.

Effects of mutual shading on the regulation of photosynthesis in field-grown sorghum

In the field, close planting inevitably causes mutual shading and depression of leaf photosynthesis. To clarify the regulative mechanisms of photosynthesis under these conditions, the effects of planting density on leaf structure, gas exchange and proteomics were carefully studied in field-grown sorghum. In the absence of mineral deficiency, (1) close planting induced a significant decrease in light intensity within populations, which further resulted in much lower stomatal density and other anatomical characteristics associated with shaded leaves; (2) sorghum grown at high planting density had a lower net photosynthetic rate and stomatal conductance than those grown at low planting density; (3) approximately 62 protein spots changed their expression levels under the high planting density conditions, and 22 proteins associated with photosynthesis were identified by mass spectrometry. Further analysis revealed the depression of photosynthesis caused by mutual shading involves the regulation of leaf structure, absorption and transportation of CO2, photosynthetic electron transport, production of assimilatory power, and levels of enzymes related to the Calvin cycle. Additionally, heat shock protein and oxygen-evolving enhancer protein play important roles in photoprotection in field-grown sorghum. A model for the regulation of photosynthesis under mutual shading was suggested based on our results.

Elucidation of salt stress defense and tolerance mechanisms of crop plants using proteomics--current achievements and perspectives

Salinity is a major threat limiting the productivity of crop plants. A clear demand for improving the salinity tolerance of the major crop plants is imposed by the rapidly growing world population. This review summarizes the achievements of proteomic studies to elucidate the response mechanisms of selected model and crop plants to cope with salinity stress. We also aim at identifying research areas, which deserve increased attention in future proteome studies, as a prerequisite to identify novel targets for breeding strategies. Such areas include the impact of plant-microbial communities on the salinity tolerance of crops under field conditions, the importance of hormone signaling in abiotic stress tolerance, and the significance of control mechanisms underlying the observed changes in the proteome patterns. We briefly highlight the impact of novel tools for future proteome studies and argue for the use of integrated approaches. The evaluation of genetic resources by means of novel automated phenotyping facilities will have a large impact on the application of proteomics especially in combination with metabolomics or transcriptomics.

Transcriptome analysis of Salicornia europaea under saline conditions revealed the adaptive primary metabolic pathways as early events to facilitate salt adaptation

BACKGROUND

Halophytes such as Salicornia europaea have evolved to exhibit unique mechanisms controlled by complex networks and regulated by numerous genes and interactions to adapt to habitats with high salinity. However, these mechanisms remain unknown.

METHODS

To investigate the mechanism by which halophytes tolerate salt based on changes in the whole transcriptome, we performed transcriptome sequencing and functional annotation by database search. Using the unigene database, we conducted digital gene expression analysis of S. europaea at various time points after these materials were treated with NaCl. We also quantified ion uptakes. Gene functional enrichment analysis was performed to determine the important pathways involved in this process.

RESULTS

A total of 57,151 unigenes with lengths of >300 bp were assembled, in which 57.5% of these unigenes were functionally annotated. Differentially expressed genes indicated that cell wall metabolism and lignin biosynthetic pathways were significantly enriched in S. europaea to promote the development of the xylem under saline conditions. This result is consistent with the increase in sodium uptake as ions pass through the xylem. Given that PSII efficiency remained unaltered, salt treatment activated the expression of electron transfer-related genes encoded by the chloroplast chromosome. Chlorophyll biosynthesis was also inhibited, indicating the energy-efficient state of the electron transfer system of S. europaea.

CONCLUSIONS

The key function of adjusting important primary metabolic pathways in salt adaption was identified by analyzing the changes in the transcriptome of S. europaea. These pathways could involve unique salt tolerance mechanisms in halophytes. This study also provided information as the basis of future investigations on salt response genes in S. europaea. Ample gene resources were also provided to improve the genes responsible for the salt tolerance ability of crops.

Proteome changes in wild and modern wheat leaves upon drought stress by two-dimensional electrophoresis and nanoLC-ESI-MS/MS

To elucidate differentially expressed proteins and to further understand post-translational modifications of transcripts, full leaf proteome profiles of two wild emmer (Triticum turgidum ssp. dicoccoides TR39477 and TTD22) and one modern durum wheat (Triticum turgidum ssp. durum cv. Kızıltan) genotypes were compared upon 9-day drought stress using two-dimensional gel electrophoresis and nano-scale liquid chromatographic electrospray ionization tandem mass spectrometry methods. The three genotypes compared exhibit distinctive physiological responses to drought as previously shown by our group. Results demonstrated that many of the proteins were common in both wild emmer and modern wheat proteomes; of which, 75 were detected as differentially expressed proteins. Several proteins identified in all proteomes exhibited drought regulated patterns of expression. A number of proteins were observed with higher expression levels in response to drought in wild genotypes compared to their modern relative. Eleven protein spots with low peptide matches were identified as candidate unique drought responsive proteins. Of the differentially expressed proteins, four were selected and further analyzed by quantitative real-time PCR at the transcriptome level to compare with the proteomic data. The present study provides protein level differences in response to drought in modern and wild genotypes of wheat that may account for the differences of the overall responses of these genotypes to drought. Such comparative proteomics analyses may aid in the better understanding of complex drought response and may suggest candidate genes for molecular breeding studies to improve tolerance against drought stress and, thus, to enhance yields.