Characterization of the Medicago truncatula cell wall proteome in cell suspension culture upon elicitation and suppression of plant defense

Specialization in a Nitrogen-Fixing Symbiosis: Proteome Differences Between Sinorhizobium medicae Bacteria and Bacteroids

Using tandem mass spectrometry (MS/MS), we analyzed the proteome of Sinorhizobium medicae WSM419 growing as free-living cells and in symbiosis with Medicago truncatula. In all, 3,215 proteins were identified, over half of the open reading frames predicted from the genomic sequence. The abundance of 1,361 proteins displayed strong lifestyle bias. In total, 1,131 proteins had similar levels in bacteroids and free-living cells, and the low levels of 723 proteins prevented statistically significant assignments. Nitrogenase subunits comprised approximately 12% of quantified bacteroid proteins. Other major bacteroid proteins included symbiosis-specific cytochromes and FixABCX, which transfer electrons to nitrogenase. Bacteroids had normal levels of proteins involved in amino acid biosynthesis, glycolysis or gluconeogenesis, and the pentose phosphate pathway; however, several amino acid degradation pathways were repressed. This suggests that bacteroids maintain a relatively independent anabolic metabolism. Tricarboxylic acid cycle proteins were highly expressed in bacteroids and no other catabolic pathway emerged as an obvious candidate to supply energy and reductant to nitrogen fixation. Bacterial stress response proteins were induced in bacteroids. Many WSM419 proteins that are not encoded in S. meliloti Rm1021 were detected, and understanding the functions of these proteins might clarify why S. medicae WSM419 forms a more effective symbiosis with M. truncatula than S. meliloti Rm1021.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Improving the Yield and Nutritional Quality of Forage Crops

Despite being some of the most important crops globally, there has been limited research on forages when compared with cereals, fruits, and vegetables. This review summarizes the literature highlighting the significance of forage crops, the current improvements and some of future directions for improving yield and nutritional quality. We make the point that the knowledge obtained from model plant and grain crops can be applied to forage crops. The timely development of genomics and bioinformatics together with genome editing techniques offer great scope to improve forage crops. Given the social, environmental and economic importance of forage across the globe and especially in poorer countries, this opportunity has enormous potential to improve food security and political stability.

Transcriptomic Profiling and Physiological Analysis of Haloxylon ammodendron in Response to Osmotic Stress

Haloxylon ammodendron, a perennial xero-halophyte, is an essential species for investigating the effects of drought on desert tree. To gain a comprehensive knowledge on the responses of H. ammodendron to drought stress, we specially performed the molecular and physiological analysis of H. ammodendron in response to -0.75 MPa osmotic stress for six and 24 h in lab condition via RNA-seq and digital gene expression (DGE). In total, 87,109 unigenes with a mean length of 680 bp and 13,486 potential simple sequence repeats (SSRs) were generated, and 3353 differentially expressed genes (DEGs) in shoots and 4564 in roots were identified under stress. These DEGs were mainly related to ion transporters, signal transduction, ROS-scavenging, photosynthesis, cell wall organization, membrane stabilization and hormones. Moreover, the physiological changes of inorganic ions and organic solute content, peroxidase (POD) activity and osmotic potential were in accordance with dynamic transcript profiles of the relevant genes. In this study, a detailed investigation of the pathways and candidate genes identified promote the research on the molecular mechanisms of abiotic stress tolerance in the xero-halophytic species. Our data provides valuable genetic resources for future improvement of forage and crop species for better adaptation to abiotic stresses.

Extraction and Characterization of Extracellular Proteins and Their Post-Translational Modifications from Arabidopsis thaliana Suspension Cell Cultures and Seedlings: A Critical Review

Proteins secreted by plant cells into the extracellular space, consisting of the cell wall, apoplastic fluid, and rhizosphere, play crucial roles during development, nutrient acquisition, and stress acclimation. However, isolating the full range of secreted proteins has proven difficult, and new strategies are constantly evolving to increase the number of proteins that can be detected and identified. In addition, the dynamic nature of the extracellular proteome presents the further challenge of identifying and characterizing the post-translational modifications (PTMs) of secreted proteins, particularly glycosylation and phosphorylation. Such PTMs are common and important regulatory modifications of proteins, playing a key role in many biological processes. This review explores the most recent methods in isolating and characterizing the plant extracellular proteome with a focus on the model plant Arabidopsis thaliana, highlighting the current challenges yet to be overcome. Moreover, the crucial role of protein PTMs in cell wall signalling, development, and plant responses to biotic and abiotic stress is discussed.

Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement

The crop legumes such as chickpea, common bean, cowpea, peanut, pigeonpea, soybean, etc. are important sources of nutrition and contribute to a significant amount of biological nitrogen fixation (>20 million tons of fixed nitrogen) in agriculture. However, the production of legumes is constrained due to abiotic and biotic stresses. It is therefore imperative to understand the molecular mechanisms of plant response to different stresses and identify key candidate genes regulating tolerance which can be deployed in breeding programs. The information obtained from transcriptomics has facilitated the identification of candidate genes for the given trait of interest and utilizing them in crop breeding programs to improve stress tolerance. However, the mechanisms of stress tolerance are complex due to the influence of multi-genes and post-transcriptional regulations. Furthermore, stress conditions greatly affect gene expression which in turn causes modifications in the composition of plant proteomes and metabolomes. Therefore, functional genomics involving various proteomics and metabolomics approaches have been obligatory for understanding plant stress tolerance. These approaches have also been found useful to unravel different pathways related to plant and seed development as well as symbiosis. Proteome and metabolome profiling using high-throughput based systems have been extensively applied in the model legume species, Medicago truncatula and Lotus japonicus, as well as in the model crop legume, soybean, to examine stress signaling pathways, cellular and developmental processes and nodule symbiosis. Moreover, the availability of protein reference maps as well as proteomics and metabolomics databases greatly support research and understanding of various biological processes in legumes. Protein-protein interaction techniques, particularly the yeast two-hybrid system have been advantageous for studying symbiosis and stress signaling in legumes. In this review, several studies on proteomics and metabolomics in model and crop legumes have been discussed. Additionally, applications of advanced proteomics and metabolomics approaches have also been included in this review for future applications in legume research. The integration of these "omics" approaches will greatly support the identification of accurate biomarkers in legume smart breeding programs.

Isolation and Analysis of Cell Wall Proteome in Elsholtzia splendens Roots Using ITRAQ with LC-ESI-MS/MS

Cell wall proteins (CWPs) are a prime site for signal perception and defense responses to environmental stresses. To gain further insights into CWPs and their molecular function, traditional techniques (e.g., two-dimensional gel electrophoresis) may be ineffective for special proteins. Elsholtzia splendens is a copper-tolerant plant species that grow on copper deposits. In this study, a fourplex isobaric tag was used for relative and absolute quantitation with liquid chromatography-tandem mass spectrometry approach to analyze the root CWPs of E. splendens. A total of 479 unique proteins were identified, including 121 novel proteins. Approximately 80.79 % of the proteins were extracted in the CaCl2 fraction, 16.08 % were detected in the NaCl fraction, and 3.13 % were identified in both fractions. The identified proteins have been involved in various processes, including cell wall remodeling, signal transduction, defense, and carbohydrate metabolism, thereby indicating a complex regulatory network in the apoplast of E. splendens roots. This study presents the first large-scale analysis of CWPs in metal-tolerant plants, which may be of paramount importance to understand the molecular functions and metabolic pathways in the root cell wall of copper-tolerant plants.

Differential protein expression of Caco-2 cells treated with selenium nanoparticles compared with sodium selenite and selenomethionine

The study was designed to determine the differential protein expression of Caco-2 cells treated with different forms of selenium including sodium selenite, selenomethionine (Se-Met), and selenium nanoparticles (nano-Se). Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS) were used to identify the differentially expressed proteins. The results indicated that seven protein spots, ubiquitin-conjugating enzyme E2 (E2), glutathione synthetases (GS), triosephosphate isomerase (TSP), T-complex protein 1 subunit zeta (TCPZ), lamin-B1, heterogeneous nuclear ribonucleoprotein F (hnRNP F), and superoxide dismutase [Cu-Zn] (Cu, Zn-SOD) were significantly different among all the groups. According to the order of control, sodium selenite, Se-Met, and Nano-Se, the expression levels of two proteins (E2 and GS) increased and the other differential proteins were reverse. Except for E2, there were no significant differences in other protein expressions between the groups treated with nano-Se and Se-Met.

Protein secretome of moss plants (Physcomitrella patens) with emphasis on changes induced by a fungal elicitor

Studies on extracellular proteins (ECPs) contribute to understanding of the multifunctional nature of apoplast. Unlike vascular plants (tracheophytes), little information about ECPs is available from nonvascular plants, such as mosses (bryophytes). In this study, moss plants (Physcomitrella patens) were grown in liquid culture and treated with chitosan, a water-soluble form of chitin that occurs in cell walls of fungi and insects and elicits pathogen defense in plants. ECPs released to the culture medium were compared between chitosan-treated and nontreated control cultures using quantitative mass spectrometry (Orbitrap) and 2-DE-LC-MS/MS. Over 400 secreted proteins were detected, of which 70% were homologous to ECPs reported in tracheophyte secretomes. Bioinformatics analyses using SignalP and SecretomeP predicted classical signal peptides for secretion (37%) or leaderless secretion (27%) for most ECPs of P. patens, but secretion of the remaining proteins (36%) could not be predicted using bioinformatics. Cultures treated with chitosan contained 72 proteins not found in untreated controls, whereas 27 proteins found in controls were not detected in chitosan-treated cultures. Pathogen defense-related proteins dominated in the secretome of P. patens, as reported in tracheophytes. These results advance knowledge on protein secretomes of plants by providing a comprehensive account of ECPs of a bryophyte.

Novel aspects of grapevine response to phytoplasma infection investigated by a proteomic and phospho-proteomic approach with data integration into functional networks

BACKGROUND

Translational and post-translational protein modifications play a key role in the response of plants to pathogen infection. Among the latter, phosphorylation is critical in modulating protein structure, localization and interaction with other partners. In this work, we used a multiplex staining approach with 2D gels to study quantitative changes in the proteome and phosphoproteome of Flavescence dorée-affected and recovered 'Barbera' grapevines, compared to healthy plants.

RESULTS

We identified 48 proteins that differentially changed in abundance, phosphorylation, or both in response to Flavescence dorée phytoplasma infection. Most of them did not show any significant difference in recovered plants, which, by contrast, were characterized by changes in abundance, phosphorylation, or both for 17 proteins not detected in infected plants. Some enzymes involved in the antioxidant response that were up-regulated in infected plants, such as isocitrate dehydrogenase and glutathione S-transferase, returned to healthy-state levels in recovered plants. Others belonging to the same functional category were even down-regulated in recovered plants (oxidoreductase GLYR1 and ascorbate peroxidase). Our proteomic approach thus agreed with previously published biochemical and RT-qPCR data which reported down-regulation of scavenging enzymes and accumulation of H2O2 in recovered plants, possibly suggesting a role for this molecule in remission from infection. Fifteen differentially phosphorylated proteins (| ratio | > 2, p < 0.05) were identified in infected compared to healthy plants, including proteins involved in photosynthesis, response to stress and the antioxidant system. Many were not differentially phosphorylated in recovered compared to healthy plants, pointing to their specific role in responding to infection, followed by a return to a steady-state phosphorylation level after remission of symptoms. Gene ontology (GO) enrichment and statistical analysis showed that the general main category "response to stimulus" was over-represented in both infected and recovered plants but, in the latter, the specific child category "response to biotic stimulus" was no longer found, suggesting a return to steady-state levels for those proteins specifically required for defence against pathogens.

CONCLUSIONS

Proteomic data were integrated into biological networks and their interactions were represented through a hypothetical model, showing the effects of protein modulation on primary metabolic ways and related secondary pathways. By following a multiplex-staining approach, we obtained new data on grapevine proteome pathways that specifically change at the phosphorylation level during phytoplasma infection and following recovery, focusing for the first time on phosphoproteome changes during pathogen infection in this host.

Heat treatment of peach fruit: modifications in the extracellular compartment and identification of novel extracellular proteins

Ripening of peach (Prunus persica L. Batsch) fruit is accompanied by dramatic cell wall changes that lead to softening. Post-harvest heat treatment is effective in delaying softening and preventing some chilling injury symptoms that this fruit exhibits after storage at low temperatures. In the present work, the levels of twelve transcripts encoding proteins involved in cell wall metabolism, as well as the differential extracellular proteome, were examined after a post-harvest heat treatment (HT; 39 °C for 3 days) of "Dixiland" peach fruit. A typical softening behaviour, in correlation with an increase in 1-aminocyclopropane-1-carboxylic acid oxidase-1 (PpACO1), was observed for peach maintained at 20 °C for 3 days (R3). Six transcripts encoding proteins involved in cell wall metabolism significantly increased in R3 with respect to peach at harvest, while six showed no modification or even decreased. In contrast, after HT, fruit maintained their firmness, exhibiting low PpACO1 level and significant lower levels of the twelve cell wall-modifying genes than in R3. Differential proteomic analysis of apoplastic proteins during softening and after HT revealed a significant decrease of DUF642 proteins after HT; as well as an increase of glyceraldehyde-3-phosphate dehydrogenase (GAPC) after softening. The presence of GAPC in the peach extracellular matrix was further confirmed by in situ immunolocalization and transient expression in tomato fruit. Though further studies are required to establish the function of DUF642 and GAPC in the apoplast, this study contributes to a deeper understanding of the events during peach softening and after HT with a focus on this key compartment.

Comparative evaluation of extraction methods for apoplastic proteins from maize leaves

Proteins in the plant apoplast are essential for many physiological processes. We have analysed and compared six different infiltration solutions for proteins contained in the apoplast to recognize the most suitable method for leaves and to establish proteome maps for each extraction. The efficiency of protocols was evaluated by comparing the protein patterns resolved by 1-DE and 2-DE, and revealed distinct characteristics for each infiltration solution. Nano-LC-ESI-Q-TOF MS analysis of all fractions was applied to cover all proteins differentially extracted by infiltration solutions and led to the identification of 328 proteins in total in apoplast preparations. The predicted subcellular protein localisation distinguished the examined infiltration solutions in those with high or low amounts of intracellular protein contaminations, and with high or low quantities of secreted proteins. All tested infiltration solution extracted different subsets of proteins, and those implications on apoplast-specific studies are discussed.

Proteomic analysis of the compatible interaction between Vitis vinifera and Plasmopara viticola

We analyzed the proteome of grapevine (Vitis vinifera) leaves 24, 48 and 96 h post infection (hpi) with the downy mildew pathogen Plasmopara viticola. Total proteins were separated on 2-DE gels. By MS analysis, we identified 82 unique grapevine proteins differentially expressed after infection. Upregulated proteins were often included in the functional categories of general metabolism and stress response, while proteins related to photosynthesis and energy production were mostly downregulated. As expected, the activation of a defense reaction was observed more often at the late time point, consistent with the establishment of a compatible interaction. Most proteins involved in resistance were isoforms of different PR-10 pathogenesis-related proteins. Although >50 differentially expressed protein isoforms were observed at 24 and 96 hpi, only 18 were detected at 48 hpi and no defense-related proteins were among this group. This profile suggests a transient breakdown in defense responses accompanying the onset of disease, further supported by gene expression analyses and by a western blot analysis of a PR-10 protein. Our data reveal the complex modulation of plant metabolism and defense responses during compatible interactions, and provide insight into the underlying molecular processes which may eventually yield novel strategies for pathogen control in the field.