Search Results (89)

Soybeans are highly susceptible to drought stress, which significantly impairs their growth and yield. Silicon (Si) supplementation has emerged as a promising strategy to mitigate drought-induced damage in plants. We investigated changes in the physiological and chloroplast proteomes in soybeans under drought stress, both with and without Si supplementation. Soybean plants were grown under controlled conditions and subjected to drought stress. The treatments included Si application (sodium silicate), sodium chloride control, and water control. Chloroplast proteins were extracted from control and Si-treated plants and analyzed using two-dimensional gel electrophoresis and mass spectrometry. Plants treated with Si showed improved drought tolerance, exhibiting reduced leaf rolling and wilting, while the control plants experienced significant wilting under drought conditions. Photosynthetic performance, measured by quantum efficiency of photosystem II and chlorophyll content, was better maintained in Si-supplemented plants under drought. However, stomatal conductance and transpiration were similarly reduced across all drought treatments. We detected 15 Si-responsive protein spots corresponding to 13 unique chloroplast proteins that were differentially expressed in response to Si supplementation. These identified proteins include those involved in photosynthesis, such as Rubisco activase isoforms, oxygen-evolving enhancer proteins, and PsbP domain-containing protein, as well as stress response proteins like dehydrin and 20 kDa chaperonin. Si treatment upregulated Rubisco activase isoforms, oxygen-evolving enhancer proteins, PsbP domain-containing protein, and 20 kDa chaperonin, which are typically reduced under drought. Si treatment maintained a higher glutamine synthetase level under drought stress. Gene ontology and KEGG pathway analyses revealed that Si-modulated proteins are associated with photosynthesis, energy metabolism, and nitrogen metabolism under drought stress. Our findings demonstrate that Si supplementation alleviates drought stress in soybean by preserving chloroplast function and enhancing the expression of photosynthetic proteins and enzymes, as well as key stress-responsive proteins. This research provides insights into the molecular mechanisms of Si-induced drought tolerance in soybeans and highlights potential targets for developing drought-resilient soybean cultivars. Full article

Cinnamomum burmanni (Nees & T. Nees) Blume, a member of the Lauraceae family, exhibits adaptability to diverse environmental conditions by synthesizing a diverse array of specialized secondary metabolites, including terpenoids and cinnamaldehyde. Nevertheless, the molecular mechanisms underlying the chemical diversity in the leaves of C. burmanni and their remarkable adaptation to subtropical and tropical forests in South China have not been thoroughly investigated. This research integrates transcriptomic and proteomic analyses across five chemotypes of C. burmanni, namely, the borneol-type (BORCB), cinnamaldehyde-type (PROCB), eucalyptol-type (EUCCB), phytol-type (PHYCB), and chlorophyllinol-type (CARCB), by means of the Nanopore and Nano UPLC-MS/MS sequencing data. The findings indicate that PROCB demonstrates an up-regulation of the phenylpropanoid pathway (such as PAL, C4H, PR proteins), which is associated with biotic stress defense. In contrast, the terpenoid-dominated chemotypes (BORCB, EUCCB, PHYCB) prioritize the biosynthesis of monoterpenes and diterpenes as well as redox homeostasis. Protein–protein interaction networks highlight functional specialization; BORCB up-regulates the expression of enzymes GGPPS and TPS2, which are involved in monoterpene production; PHYCB enhances the activity of diterpene synthases (CPS, KSL) and chloroplast retrograde signaling; EUCCB activates SOD/GST to mitigate oxidative stress. PROCB induced defense hubs (NPR1, WRKY33) mediated by salicylic acid and pathogenesis-related proteins. The study establishes a comprehensive multi-omics resource for a gene–protein–metabolite framework, elucidating the mechanisms of stress resilience of C. burmanni in South China. Full article

Maize (Zea mays L.), as a globally significant cereal crop, exhibits high sensitivity to salt stress during early seedling stages. Although melatonin (MT) has demonstrated potential in mitigating abiotic stresses, the specific mechanisms underlying MT-mediated alleviation of salt stress in maize seedlings remain unclear. In this study, we established four treatment groups: control (CK), melatonin treatment (MT), salt stress (NaCl), and combined treatment (NaCl_MT). Metabolomic and proteomic analyses were performed, supplemented by photosynthesis-related experiments as well as antioxidant-related experiments. Metabolomic analysis identified key metabolites in MT-mediated salt stress mitigation. Both metabolomic and proteomic analyses underscored the critical roles of photosynthetic and antioxidant pathways. Salt stress significantly decreased the net photosynthetic rate (Pn) by 67.7%, disrupted chloroplast ultrastructure, and reduced chlorophyll content by 41.6%. Conversely, MT treatment notably mitigated these detrimental effects. Moreover, MT enhanced the activities of antioxidant enzymes by approximately 10–20% and reduced the accumulation of oxidative stress markers by around 10–25% in maize seedlings under salt stress. In conclusion, this study conducted a systematic and multidimensional investigation into the mitigation of salt stress in maize seedlings by MT. Our results revealed that MT enhances antioxidant systems, increases chlorophyll content, and alleviates damage to chloroplast ultrastructure, thereby improving photosystem II performance and strengthening photosynthesis. This ultimately manifests as improved seedling phenotypes under salt stress. These findings provide a meaningful entry point for breeding salt-tolerant maize varieties and mitigating the adverse effects of salinized soil on maize growth and yield. Full article

Proteomic profiling using ultrafast chromatography–mass spectrometry provides valuable insights into plant responses to abiotic factors by linking molecular changes with physiological outcomes. Nanopriming, a novel approach involving the treatment of seeds with nanoparticles, has demonstrated potential for enhancing plant metabolism and productivity. However, the molecular mechanisms underlying nanoparticle-induced effects remain poorly understood. In this study, we investigated the impact of gold nanoparticle (Au-NP) seed priming on the proteome of wheat (Triticum aestivum L.) seedlings. Differentially regulated proteins (DRPs) were identified, revealing a pronounced reorganization of the photosynthetic apparatus (PSA). Both the light-dependent reactions and the Calvin cycle were affected, with significant upregulation of chloroplast-associated protein complexes, including PsbC (CP43), chlorophyll a/b-binding proteins, Photosystem I subunits (PsaA and PsaB), and the γ-subunit of ATP synthase. The large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCo) exhibited over a threefold increase in expression in Au-NP-treated seedlings. The proteomic changes in the large subunit RuBisCo L were corroborated by transcriptomic data. Importantly, the proteomic changes were supported by physiological and biochemical analyses, ultrastructural modifications in chloroplasts, and increased photosynthetic activity. Our findings suggest that Au-NP nanopriming triggers coordinated molecular responses, enhancing the functional activity of the PSA. Identified DRPs may serve as potential biomarkers for further elucidation of nanopriming mechanisms and for the development of precision strategies to improve crop productivity. Full article

Background: Membrane proteins are preferentially solubilized with sodium dodecyl sulfate (SDS), which necessitates a purification protocol to deplete the surfactant prior to mass spectrometry analysis. However, maintaining solubility of intact membrane proteins is challenged in an SDS-free environment. SDS precipitation with potassium salts (KCl) offers a potentially viable workflow to deplete SDS and permit proteoform analysis. The purpose of this study is to devise a robust detergent-based protocol applicable for processing and analysis of intact membrane-associated proteoforms. Methods: The precipitation conditions impacting SDS removal from spinach chloroplasts and liver membrane proteome preparations were evaluated, capitalizing on optimization of pH (highly basic), addition of MS-compatible solubilizing additives (urea) and adjustment of the KCl to SDS ratio to maximize recovery and purity. Results: Characterization of the SDS-solubilized, KCl-precipitated spinach membrane preparation revealed multiple charge envelope MS spectra displaying high signal to noise, free of SDS adducts. Precipitation at pH 12 or with urea improved protein recovery and purity. Bottom-up analysis identified 1826 distinct liver protein groups from four independent SDS precipitation conditions. While precipitation at pH 8 without urea revealed a greater number of protein identifications by mass spectrometry, precipitation under highly basic conditions (pH 12) with urea provided higher membrane protein recovery and achieved the greatest number (732 of 1056) and largest percentage (69.3%) of membrane proteins identified in the SDS removal workflow. Conclusion: This workflow provides new opportunities for MS-based proteoform analysis by capitalizing on the benefits of SDS for protein extraction while maintaining high solubility and purity of intact proteins though KCl precipitation of the surfactant. Full article

Tomato brown rugose fruit virus (ToBRFV) is an important emerging virus that poses a serious threat to the global agricultural economy. Ubiquitination is one of the key post-translational protein modification types in plant responses to biotic stress, but the extent to which ToBRFV infection alters the overall ubiquitination status has not been reported. This study conducted integrated ubiquitome and proteome analyses of Nicotiana benthamiana leaves infected with ToBRFV and identified differentially ubiquitinated proteins. A total of 346 lysine sites on 302 identified proteins were found to be affected, with 260 sites exhibiting upregulated ubiquitination levels in 224 proteins and 86 sites showing downregulated ubiquitination levels in 80 proteins. The differentially ubiquitinated proteins were primarily localized in the cytoplasm (29%), nucleus (18%), plasma membrane (8.9%), mitochondria (5.1%), and chloroplasts (4.6%). Fourteen conserved ubiquitination motifs, including ENNNK, ENNK, SK, and KNG, were identified. Furthermore, enrichment analysis indicated that ToBRFV infection induces an increase in the ubiquitination levels of proteins associated with ion transport, MAPK signaling pathways, and plant hormone signal transduction, while the ubiquitination levels of proteins related to carbon metabolism and secondary metabolite synthesis decreased. Functional analysis of the three differentially ubiquitinated proteins revealed that a RING/U-box superfamily protein negatively regulates ToBRFV infection. Our work provides the first systematic analysis of the ubiquitination profile in N. benthamiana leaves following ToBRFV infection, providing important resources for further studies on the regulatory mechanisms of ubiquitination in plant responses to ToBRFV. Full article

Desert shrubs play an important role in the stability of arid and fragile desert ecosystems. However, despite their significant ecological importance, limited research has been performed on shrub drought tolerance strategies at the morphological, physiological, and molecular levels. Therefore, this study focused on the typical desert shrub, Calligonum leucocladum, and analyzed its morphology, physiology, and protein expression under two different habitats: moist low-salt and arid low-salt. The results indicate that drought stress inhibited the growth of C. leucocladum, leading to significant reductions in its plant height, base diameter, and crown width by 14.93%, 49.57%, and 48.49%, respectively. Drought stress triggered a 30% decline in stomatal conductance, whereas homeostasis was observed in net photosynthesis, intercellular CO₂, and transpiration. The soluble sugar content significantly increased by 13.43%, while the starch, soluble protein, and proline content significantly decreased by 20.32%, 10.67%, and 55.61%, respectively. In addition, under drought stress, membrane peroxidation products, reactive oxygen species metabolites, and antioxidant enzyme activities significantly increased. Weighted gene co-expression network analysis revealed 40 proteins that were significantly enriched in the photosynthesis and oxidative phosphorylation pathways through KEGG enrichment analysis. In addition, C. leucocladum maintains photosynthetic homeostasis by enhancing PSII repair (PsbE, PsbL, PsbH) and electron transfer chain efficiency (PetD, nad 2, nad 9), thereby compensating for the insufficient carbon dioxide supply caused by stomatal limitation. This study integrated multidimensional data from morphology, physiology, and proteomics to reveal that C. leucocladum drives a coupled network of photosynthesis, antioxidant, and carbon metabolism through chloroplast translation reprogramming. It maintains photosynthetic homeostasis and osmotic balance under a 30% decrease in stomatal conductance, elucidating the cross-scale regulatory strategy of desert shrubs adapting to extreme drought. Full article

Chloroplasts are important in plant growth, development, and defense mechanisms, making them central to addressing global agricultural challenges. This review explores the multi-faceted contributions of chloroplasts, including photosynthesis, hormone biosynthesis, and stress signaling, which orchestrate the trade-off between growth and defense. Advancements in chloroplast genomics, transcription, translation, and proteomics have deepened our understanding of their regulatory functions and interactions with nuclear-encoded proteins. Case studies have demonstrated the potential of chloroplast-targeted strategies, such as the expression of elongation factor EF-2 for heat tolerance and flavodiiron proteins for drought resilience, to enhance crop productivity and stress adaptation. Future research directions should focus on the need for integrating omics data with nanotechnology and synthetic biology to develop sustainable and resilient agricultural systems. This review uniquely integrates recent advancements in chloroplast genomics, transcriptional regulation, and synthetic biology to present a holistic perspective on optimizing plant growth and stress tolerance. We emphasize the role of chloroplast-driven trade-off in balancing growth and immunity, leveraging omics technologies and emerging biotechnological innovations. This comprehensive approach offers new insights into sustainable agricultural practices, making it a significant contribution to the field. Full article

In metabolically engineered plants, the target products are usually uniformly distributed in the whole plant or specific tissues. When engineering tobacco to produce astaxanthin, a ketocarotenoid with strong antioxidant activity and multiple bioactivities, a scattered distribution of astaxanthin-producing regions was observed in a small portion of astaxanthin-producing tobacco plants, which caused mosaic-like red and green spots on the leaves (ASTA-mosaic). A physiological assay showed that the non-astaxanthin green region (Mosaic_G) had relatively higher chlorophyll content and better chloroplast structure than the astaxanthin-producing red region (Mosaic_R). Then, metabolomics, proteomics, and small RNA transcriptomics were employed to analyze the uneven distribution of astaxanthin-producing regions in tobacco leaves. The results of metabolomics and proteomics revealed a decrease in carotenoid metabolism, chlorophyll biosynthesis, and chlorophyll degradation in the Mosaic_G region. Pheophorbide a, an intermediate of chlorophyll degradation, was found to be significantly reduced in the Mosaic_G region, which was accompanied by the attenuation of chlorophyllase and pheophytinase, which catalyze the formation of pheophorbide a in chlorophyll degradation. Reductions in photosynthetic antenna proteins and photosystem-associated proteins were observed in the Mosaic_R region, consistent with the better chloroplast structure of the Mosaic_G region. Small RNA transcriptomics showed that several small RNAs could target chlorophyll-degradative genes, but they were more effective in targeting the astaxanthin biosynthetic genes. This finding was supported by the fact that the Mosaic_G region can remain green up to the senescence of tobacco leaves. This work provides insights into the mechanism of the uneven distribution of astaxanthin-producing regions in tobacco leaves and may contribute to the specialized utilization of tobacco plants for metabolic engineering. Full article

The paramount objectives of this study were to analyze the beneficial role of the circadian clock in alleviating drought stress in an essential green leafy horticultural crop, spinach (Spinacia oleracea), and to attain knowledge on drought-stress adaptation for crop productivity. From dawn to dusk, a circadian core oscillator-based defense mechanism was noticed in relation to the strength of the chloroplast proteome and transcriptome, and the defense hormone fused it along with the molecular physiology using genotypes “Malav Jyoti” and “Delhi Green”. A photo-periodic rhythmicity containing a 4 h time interval (morning–evening loop) for 12 h in spinach was exhibited under drought-stressed (day-5) and drought re-irrigated (day-10) conditions. The circadian oscillator controlled 70% of the major part of growth and physiological measures such as the biomass, plant height, leaf-relative water content, and the shoot–root ratio under drought stress. Contrarily, drought stress resulted in the upregulation of antioxidative activities and stress markers, whereas it was diversified and maintained in the case of the re-irrigated state at certain rhythmic time intervals of the circadian clock. The physiological parameters we examined, such as net photosynthesis, transpiration, stomatal conductance, and antioxidative enzymes, exhibited the role of the circadian clock in drought stress by showing 80–90% improvements found in plants when they were re-watered after drought stress based on their circadian oscillations. Based on the physiological results, 10 a.m. and 2 p.m. were disclosed to be the rhythmic times for controlling drought stress. Moreover, an extensive study on a gene expression analysis of circadian clock-based genes (CCA1, LHY, TOC1, PRR3, PRR5, PRR7, PRR9, and RVE8) and drought-responsive genes (DREB1, DREB2, and PIP1) depicted the necessity of a circadian oscillator in alleviating drought stress. Hence, the findings of our study allowed for an intense understanding of photo-periodic rhythms in terms of the morning–evening loop, which is in line with the survival rate of spinach plants and occurs by altering cellular ROS-scavenging mechanisms, chloroplast protein profiles, gene regulation, and metabolite concentrations. Full article

Although the mechanisms underlying albino phenotypes have been examined in model plants and major crops, our knowledge of bract albinism is still in its infancy. Davidia involucrata, a relic plant called dove tree, is best known for the intriguing trait with a pair of white bracts covering the capitula. Here, comparative physiological, cytological, proteomic, and metabolomic analyses were performed to dissect the albinism mechanism of D. involucrata bracts. The bracts exhibited low chlorophyll and carotenoid contents, reduced photosynthetic efficiency, and impaired chloroplast structure. The severe deficiency of photosynthetic pigments and the substantial decrease in cuticle thickness made the bracts light-sensitive. In total, 1134 differentially expressed proteins (DEPs) were obtained between bracts and leaves. Pathway enrichment analysis of DEPs revealed that photosynthetic pigment biosynthesis and photosynthesis were suppressed, whereas protein processing in endoplasmic reticulum, flavonoid biosynthesis, and the ubiquitin–proteasome system (UPS) were activated in bracts. Strikingly, DEPs implicated in chloroplast development, including PPR and AARS proteins, were mainly down-regulated in bracts. We further investigated albinism-induced metabolic changes and detected 412 differentially abundant metabolites (DAMs). Among them, enhanced flavonoids accumulation can plausibly explain the role of bracts in pollinator attraction. Amino acids and their derivatives in bracts showed remarkably increased abundance, which might be causally linked to enhanced UPS function. Our work could lay foundations for understanding albinism mechanisms and adaptive significance of plant bracts and facilitate future utilization of D. involucrata resources. Full article

Stress on the Endoplasmic reticulum (ER) can severely disrupt cellular function by impairing protein folding and post-translational modifications, thereby leading to the accumulation of poor-quality proteins. However, research on its impact on photosynthesis remains limited. In this study, we investigated the impact of ER stress on the photosynthetic efficiency of Chlamydomonas reinhardtii using pharmacological inducers, tunicamycin (TM) and brefeldin A (BFA), which specifically target the ER. Our measurements of photosynthetic parameters showed that these ER stress-inducing compounds caused a significant decline in photosynthetic efficiency. A proteomic analysis confirmed that TM and BFA effectively induce ER stress, as evidenced by the upregulation of ER stress-related proteins. Furthermore, we observed a widespread downregulation of photosynthesis-related proteins, which is consistent with the results obtained from our measurements of photosynthetic parameters. These findings suggest that the stress on ER has a profound impact on chloroplast function, disrupting photosynthetic processes. This study highlights the critical interdependence between the ER and chloroplasts, and it underscores the broader implications of ER stress on the cellular metabolism and energy efficiency of photosynthetic organisms. Full article

The bread wheat cultivar (Triticum aestivum L. cv. Sagittario) as a parental line and its mutant, drought-tolerant lines (Mutant lines 4 and 5) were subjected to polyethylene glycol (PEG)-induced drought. Drought stress resulted in decreased chlorophyll levels and the accumulation of proline and TBARS, despite increases in activities of catalase, peroxidase, and superoxide dismutase enzymes. Transcription of the genes encoding these enzymes and delta-1-pyrroline 5-carboxylase synthetase was induced by drought. 2-DE gel electrophoresis analysis identified differentially expressed proteins (DEPs) in the mutant lines, which are distinguished by “chloroplast”, “mitochondrion”, “pyruvate dehydrogenase complex”, and “homeostatic process” terms. The drought tolerance of the mutant lines might be attributed to improved photosynthesis, efficient ATP synthesis, and modified antioxidant capacity. In addition to proteomics data, the drought tolerance of wheat genotypes might also be assessed by chlorophyll content and TaPOX gene expression. To our knowledge, this is the first proteomic analysis of gamma-induced mutants of bread wheat. These findings are expected to be utilized in plant breeding studies. Full article

Isoprene, a lipophilic and unstable compound with the chemical formula C5H8, is transported to plant chloroplasts via the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway, which relies on photosynthesis. Although only about 20% of terrestrial plants can synthesize isoprene, those that emit it are more adaptable to oxidative and thermal stresses. To shed light on the still-elusive protective mechanism of isoprene, numerous investigations have been conducted. Isoprene has been shown to react with and quench various reactive oxygen species (ROS) such as singlet oxygen (1O2). Its reduced state and conjugated double bonds suggest that it functions as an antioxidant, although this has yet to be conclusively proven. Despite its low abundance relative to other molecules in plant tissues, recent research has explored several potential roles for isoprene including acting as a scavenger of ROS by serving as an antioxidant; strengthening cell membranes; modulating genomic, proteomic and metabolomic profiles; signaling stress responses among neighboring plants compared with other volatile organic compounds (VOCs); regulating metabolic fluxes of hormones produced through the MEP pathway; or even functioning as a free developmental hormone. Future prospective studies, such as identifying the specific receptors for VOCs along with transcription factors (TFs) and other regulatory proteins participating in the signaling pathways and also metabolomic, transcriptomic and physiological analyses could help in comprehending VOC-induced defense responses in plants under stress conditions. Full article

The serine peptidase CLPP is conserved among bacteria, chloroplasts, and mitochondria. In humans and mice, its loss causes Perrault syndrome, which presents with growth deficits, infertility, deafness, and ataxia. In the filamentous fungus Podospora anserina, CLPP loss leads to longevity. CLPP substrates are selected by CLPX, an AAA+ unfoldase. CLPX is known to target delta-aminolevulinic acid synthase (ALAS) to promote pyridoxal phosphate (PLP) binding. CLPX may also influence cofactor association with other enzymes. Here, the evaluation of P. anserina metabolomics highlighted a reduction in arginine/histidine levels. In Mus musculus cerebellum, reductions in arginine/histidine and citrulline occurred with a concomitant accumulation of the heme precursor protoporphyrin IX. This suggests that the increased biosynthesis of 5-carbon (C5) chain deltaALA consumes not only C4 succinyl-CoA and C1 glycine but also specific C5 delta amino acids. As enzymes responsible for these effects, the elevated abundance of CLPX and ALAS is paralleled by increased OAT (PLP-dependent, ornithine delta-aminotransferase) levels. Possibly as a consequence of altered C1 metabolism, the proteome profiles of P. anserina CLPP-null cells showed strong accumulation of a methyltransferase and two mitoribosomal large subunit factors. The reduced histidine levels may explain the previously observed metal interaction problems. As the main nitrogen-storing metabolite, a deficiency in arginine would affect the urea cycle and polyamine synthesis. Supplementation of arginine and histidine might rescue the growth deficits of CLPP-mutant patients. Full article