GeLC-Orbitrap/MS and 2-DE-MALDI-TOF/TOF comparative proteomics analysis of seed cotyledons from the non-orthodox Quercus ilex tree species

Gel electrophoresis-based and shotgun approaches are the most employed proteomic platforms in plant biology research, with the latter replacing the former in the last years. We have compared 2-DE-MALDI-TOF/TOF and GeLC-Orbitrap/MS analyses using the same protein extracts from Quercus ilex cotyledons at different development stages. The results obtained (ProteomeXchange available data, PXD020603) showed that both platforms were complementary, showing common and specific proteins identified in each case, but leading to similar biological conclusions. Protein analysis identified 562 spots in gel-based (292 variables) and 2409 proteins in shotgun (560 variables), that were detected with both platforms and represent common key pathways related to maturation and germination. The main differences concern hormone metabolism, storage and late embryogenesis abundant proteins. Deeper proteome coverage was obtained with the shotgun approach, with a greater number of metabolic pathways represented, as gibberellin biosynthesis, not observed in the gel-based analysis. Nevertheless, several storage proteins, highly abundant in cotyledons and well represented in gel-based platform were not identified using the shotgun platform. These results support that when analyzing any plant biological process, the use of both platforms is complementary rather than redundant, that favors an in-depth proteomic analysis and a more confident biological interpretation of the data obtained.

A new practical approach for the biological treatment of a mixture of cheese whey and white wastewaters using Kefir grains

Kefir grains are a microbial consortium of different genera of bacteria and yeasts. In this study, the performance of Tunisian Kefir grains during the biological treatment of a mixture of Gouda cheese whey and white wastewaters (GCW) in ratio 1:1 with very high organic matter concentration is investigated. The biological process was evaluated and optimized through the response surface methodology. Under the optimum conditions, Kefir grains concentration of 1.02%, temperature at 36.68 °C, and incubation time of 5.14 days, the removal efficiencies of COD, PO₄^3-, and NO₃^- were 87, 37.48, and 39.5%, respectively. Interestingly, the reusability tests of the grains proved not only their high resistance to harsh environmental conditions but also their great potential for more practical applications. Particularly, different strains were isolated from the grains and identified as Kluyveromyces marxianus, Lactoccocus lactis, Lactobacillus kefiri, and Bacillus spp. using 16S rDNA sequence analysis and rep-PCR fingerprinting. At the biological level, the raw GCW (RGCW) has a negative impact on the Hordeum vulgare both on seed germination, and on the growth parameters of seedlings. Interestingly, after Kefir grains treatment, the treated GCW (TGCW) allow a seedlings growth and germination rate similar to those soaked in water.

Proteomics, Holm Oak (Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other?

Proteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as Quercus, Pines, Poplars, and Eucalyptus. This review assesses the potential and limitations of the proteomics approaches and is focused on Quercus ilex as a model species and other forest tree species. Proteomics has been used with Q. ilex since 2003 with the main aim of examining natural variability, developmental processes, and responses to biotic and abiotic stresses as in other species of the genus Quercus or Pinus. As with the progress in techniques in proteomics in other plant species, the research in Q. ilex moved from 2-DE based strategy to the latest gel-free shotgun workflows. Experimental design, protein extraction, mass spectrometric analysis, confidence levels of qualitative and quantitative proteomics data, and their interpretation are a true challenge with relation to forest tree species due to their extreme orphan and recalcitrant (non-orthodox) nature. Implementing a systems biology approach, it is time to validate proteomics data using complementary techniques and integrate it with the -omics and classical approaches. The full potential of the protein field in plant research is quite far from being entirely exploited. However, despite the methodological limitations present in proteomics, there is no doubt that this discipline has contributed to deeper knowledge of plant biology and, currently, is increasingly employed for translational purposes.

Protein profile of cotyledon, tegument, and embryonic axis of mature acorns from a non-orthodox plant species: Quercus ilex

Contrary to the orthodox seeds, recalcitrant Holm oak seeds possess the enzymatic machinery to start germination during the maturation phase. The protein profile of the different parts, mature seeds, of the Holm oak, a non-orthodox plant species, has been characterized using one- and two-dimensional gel electrophoresis coupled to matrix-assisted laser desorption ionization-time of flight mass spectrometry. Protein content and profiles of the three seed tissues (cotyledon, embryonic axis and tegument) were quite different. The embryonic axis showed 4-fold and 20-fold higher protein content than the cotyledon and the tegument, respectively. Two hundred and twenty-six variable proteins among the three seed parts were identified, being classified according to their function into eight main groups. The cotyledon presented the highest number of metabolic and storage proteins (89% of them are legumin) compared to the embryonic axis and tegument. The embryonic axis had the highest number of the species within the protein fate group. The tegument presented the largest number of the defense-/stress-related and cytoskeleton proteins. This distribution is in good agreement with the biological role of the tissues. The study of the seed tissue proteome demonstrated a compartmentalization of pathways and a division of metabolic tasks between embryonic axis, cotyledon and tegument. This compartmentalization uncovered in our study should provide a starting point for understanding, at the molecular level, the particularities of the recalcitrant seeds.

Physiological and proteomics analyses of Holm oak (Quercus ilex subsp. ballota [Desf.] Samp.) responses to Phytophthora cinnamomi

Phytophthora cinnamomi is one of the agents that trigger the decline syndrome in Quercus spp., this being a serious threat to Mediterranean Holm oak forest sustainability and reforestation programs. Quercus ilex responses to Phytophthora cinnamomi have been studied in one-year olds seedlings from two Andalucía provenances, assessing the physiological water status and photosynthesis-related parameters. Upon inoculation with mycelium a reduction in water content, chlorophyll fluorescence, stomatal conductance and gas exchange was observed along a 90 days post inoculation period in both provenances. The reduction was higher in the most susceptible (SSA) provenance, than in the most tolerant (PCO), being these typical plant responses to drought stress. Leaf protein profiles were analyzed in non-inoculated and inoculated seedlings from the two provenances by using a 2-DE coupled to MS proteomics strategy. Ninety seven proteins changing in abundance in response to the inoculation were successfully identified after MALDI-TOF-TOF analyses. The largest group of variable identified proteins were chloroplasts ones, and they were involved in the photosynthesis, Calvin cycle and carbohydrate metabolism. It was noted that a general tendency was a decrease in the protein abundance as a consequence of the inoculation, being it less accused in the least susceptible, the Northern provenance (PCO), than in the most susceptible, the Southern provenance (SSA). This trend is clearly manifested in photosynthesis, amino acid metabolism and stress/defence proteins. On the contrary, some proteins related to starch biosynthesis, glycolysis and stress related peroxiredoxin showed an increase upon inoculation. These changes in protein abundance were correlated to the estimated physiological parameters and have been frequently observed in plants subjected to drought stress.

Proteomics analysis of date palm leaves affected at three characteristic stages of brittle leaf disease

Proteomics analysis has been performed in leaf tissue from field date palm trees showing the brittle leaf disease (BLD) or maladie des feuilles cassantes, the main causal agent of the date palm decline in south Tunisia. To study the evolution of the disease, proteins from healthy and affected leaves taken at three disease stages (S1, S2 and S3) were trichloroacetic acid acetone extracted and subjected to two-dimensional gel electrophoresis (5-8 pH range). Statistical analysis showed that the protein abundance profile is different enough to differentiate the affected leaves from the healthy ones. Fifty-eight variable spots were successfully identified by matrix-assisted laser desorption ionization time of flight, 60 % of which corresponded to chloroplastic ones being involved in the photosynthesis electronic chain and ATP synthesis, metabolic pathways implicated in the balance of the energy, and proteases. Changes in the proteome start at early disease stage (S1), and are greatest at S2. In addition to the degradation of the ribulose-1.5-bisphosphate carboxylase oxygenase in affected leaflets, proteins belonging to the photosynthesis electronic chain and ATP synthesis decreased following the disease, reinforcing the relationship between BLD and manganese deficiency. The manganese-stabilizing proteins 33 kDa, identified in the present work, can be considered as protein biomarkers of the disease, especially at early disease step.

Abscisic acid and sucrose increase the protein content in date palm somatic embryos, causing changes in 2-DE profile

Various supplements (abscisic acid (ABA) or sucrose) were added to the initial embryo culture medium (M3) with the aim of improving the vigour of vitroplants deriving from date palm somatic embryogenesis. ABA (20 and 40 microM) and sucrose (90 g/l) applied for 4 and 2 weeks respectively increased embryo thickness, with no apparent difference in length. ABA (5-40 microM) increased embryo proliferation rate. Somatic embryos maintained in modified M3 (M3 supplemented with ABA and an increased sucrose concentration) contained a higher amount of protein than those maintained in initial M3 (no ABA, 30 g/l of sucrose), with a 1.5-1.7-fold increase depending on the compound and concentration assayed. The 1-D and 2-DE protein profiles showed qualitative and quantitative differences between the somatic embryos cultured in initial M3 (control) and in modified M3. Statistical analysis of spot intensity was performed by principal component analysis, yielding two accurate groups of samples and determining the most discriminating spots. Samples were also clustered using Euclidean distance with an average linkage algorithm. Thirty-four variable spots were identified using mass spectrometry analysis. Identified proteins were classified into the following functional categories: energy metabolism (five proteins); protein translation, folding and degradation (9); redox maintenance (5); cytoskeleton (3); storage protein (2); and with no assigned function as (10). While "up-regulation" of stress-related proteins and "down-regulation" of energy metabolism proteins were observed in somatic embryos matured in M3 supplemented with ABA, storage proteins (legumin) were "up-regulated" in somatic embryos matured in M3 supplemented with increased sucrose.