Proteome profiling of flax (Linum usitatissimum) seed: characterization of functional metabolic pathways operating during seed development

Molecular Characterization of Adhesives (Glue Lining Pastes) Used in Restoration

The molecular characterization of samples from works of art can provide valuable insights into the composition of ancient restoration materials and their conservation state. Here, we present a novel analytical protocol for the molecular characterization of a specific adhesive used in historical painting restoration, known as "glue lining pastes." Due to the high molecular complexity of these adhesives, we propose a multistep extraction protocol to recover and fractionate from a single microsample the three main classes of biomolecules contained in glue pastes (lipids, polysaccharides, and proteins). High-performance separation coupled with high-resolution mass spectrometry (MS) techniques were applied to the isolated fractions to identify specific components. The proposed method was optimized using test specimens of various traditional glue pastes applied to canvases and successfully applied to a historical glue paste sample from the 17th-century painting "La fuga in Egitto," part of the Pagliara collection at the University Suor Orsola Benincasa (Naples, Italy). The data collected in this work provide insights into the specific recipe used for adhesive preparation, supporting artistic and historical interpretations and contributing to a broader understanding of old restoration practices. Data are available via ProteomeXchange with the identifier PXD051480.

Proteomic Profile of Flaxseed (Linum usitatissimum L.) Products as Influenced by Protein Concentration Method and Cultivar

The research is focused on the quantitative evaluation of the flaxseed (Linum usitatissimum L.) proteome at the level of seed cake (SC), fine flour-sieved a fraction below 250 µm (FF)-and protein concentrate (PC). The evaluation was performed on three oilseed flax cultivars (Agriol, Raciol, and Libra) with different levels of α-linolenic acid content using LC-MS/MS (shotgun proteomics) analysis, which was finalized by database searching using the NCBI protein database for Linum usitatissimum and related species. A total of 2560 protein groups (PGs) were identified, and their relative abundance was calculated. A set of 33 quantitatively most significant PGs was selected for further characterization. The selected PGs were divided into four classes-seed storage proteins (11S globulins and conlinins), oleosins, defense- and stress-related proteins, and other major proteins (mainly including enzymes). Seed storage proteins were found to be the most abundant proteins. Specifically, 11S globulins accounted for 41-44% of SC proteins, 40-46% of FF proteins, and 72-84% of PC proteins, depending on the cultivar. Conlinins (2S albumins) were the most abundant in FF, ranging from 10 to 13% (depending on cultivar). The second most important class from the point of relative abundance was oleosins, which were represented in SC and FF in the range of 2.1-3.8%, but only 0.36-1.20% in PC. Surprisingly, a relatively high abundance of chitinase was found in flax products as a protein related to defence and stress reactions.

Anti-Cancer Properties of Flaxseed Proteome

Flaxseed has been recognized as a valuable source of nutrients and bioactive compounds, including proteins that possess various health benefits. In recent years, studies have shown that flaxseed proteins, including albumins, globulins, glutelin, and prolamins, possess anti-cancer properties. These properties are attributed to their ability to inhibit cancer cell proliferation, induce apoptosis, and interfere with cancer cell signaling pathways, ultimately leading to the inhibition of metastasis. Moreover, flaxseed proteins have been reported to modulate cancer cell mechanobiology, leading to changes in cell behavior and reduced cancer cell migration and invasion. This review provides an overview of the anti-cancer properties of flaxseed proteins, with a focus on their potential use in cancer treatment. Additionally, it highlights the need for further research to fully establish the potential of flaxseed proteins in cancer therapy.

13C-Metabolic Flux Analysis in Developing Flax (Linum usitatissinum L.) Embryos to Understand Storage Lipid Biosynthesis

Flax (Linum usitatissinum L.) oil is an important source of α-linolenic (C18:3 ω-3). This polyunsaturated fatty acid is well known for its nutritional role in human and animal diets. Understanding storage lipid biosynthesis in developing flax embryos can lead to an increase in seed yield via marker-assisted selection. While a tremendous amount of work has been done on different plant species to highlight their metabolism during embryo development, a comprehensive analysis of metabolic flux in flax is still lacking. In this context, we have utilized in vitro cultured developing embryos of flax and determined net fluxes by performing three complementary parallel labeling experiments with 13C-labeled glucose and glutamine. Metabolic fluxes were estimated by computer-aided modeling of the central metabolic network including 11 cofactors of 118 reactions of the central metabolism and 12 pseudo-fluxes. A focus on lipid storage biosynthesis and the associated pathways was done in comparison with rapeseed, arabidopsis, maize and sunflower embryos. In our hands, glucose was determined to be the main source of carbon in flax embryos, leading to the conversion of phosphoenolpyruvate to pyruvate. The oxidative pentose phosphate pathway (OPPP) was identified as the producer of NADPH for fatty acid biosynthesis. Overall, the use of 13C-metabolic flux analysis provided new insights into the flax embryo metabolic processes involved in storage lipid biosynthesis. The elucidation of the metabolic network of this important crop plant reinforces the relevance of the application of this technique to the analysis of complex plant metabolic systems.

A Cell Wall Proteome and Targeted Cell Wall Analyses Provide Novel Information on Hemicellulose Metabolism in Flax

Experimentally-generated (nanoLC-MS/MS) proteomic analyses of four different flax organs/tissues (inner-stem, outer-stem, leaves and roots) enriched in proteins from 3 different sub-compartments (soluble-, membrane-, and cell wall-proteins) was combined with publically available data on flax seed and whole-stem proteins to generate a flax protein database containing 2996 nonredundant total proteins. Subsequent multiple analyses (MapMan, CAZy, WallProtDB and expert curation) of this database were then used to identify a flax cell wall proteome consisting of 456 nonredundant proteins localized in the cell wall and/or associated with cell wall biosynthesis, remodeling and other cell wall related processes. Examination of the proteins present in different flax organs/tissues provided a detailed overview of cell wall metabolism and highlighted the importance of hemicellulose and pectin remodeling in stem tissues. Phylogenetic analyses of proteins in the cell wall proteome revealed an important paralogy in the class IIIA xyloglucan endo-transglycosylase/hydrolase (XTH) family associated with xyloglucan endo-hydrolase activity.Immunolocalisation, FT-IR microspectroscopy, and enzymatic fingerprinting indicated that flax fiber primary/S1 cell walls contained xyloglucans with typical substituted side chains as well as glucuronoxylans in much lower quantities. These results suggest a likely central role of xyloglucans and endotransglucosylase/hydrolase activity in flax fiber formation and cell wall remodeling processes.

Proteomics in commercial crops: An overview

Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement.

SIGNIFICANCE

Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.

India's Computational Biology Growth and Challenges

India's computational science is growing swiftly due to the outburst of internet and information technology services. The bioinformatics sector of India has been transforming rapidly by creating a competitive position in global bioinformatics market. Bioinformatics is widely used across India to address a wide range of biological issues. Recently, computational researchers and biologists are collaborating in projects such as database development, sequence analysis, genomic prospects and algorithm generations. In this paper, we have presented the Indian computational biology scenario highlighting bioinformatics-related educational activities, manpower development, internet boom, service industry, research activities, conferences and trainings undertaken by the corporate and government sectors. Nonetheless, this new field of science faces lots of challenges.

Fusarium oxysporum mediates systems metabolic reprogramming of chickpea roots as revealed by a combination of proteomics and metabolomics

Molecular changes elicited by plants in response to fungal attack and how this affects plant-pathogen interaction, including susceptibility or resistance, remain elusive. We studied the dynamics in root metabolism during compatible and incompatible interactions between chickpea and Fusarium oxysporum f. sp. ciceri (Foc), using quantitative label-free proteomics and NMR-based metabolomics. Results demonstrated differential expression of proteins and metabolites upon Foc inoculations in the resistant plants compared with the susceptible ones. Additionally, expression analysis of candidate genes supported the proteomic and metabolic variations in the chickpea roots upon Foc inoculation. In particular, we found that the resistant plants revealed significant increase in the carbon and nitrogen metabolism; generation of reactive oxygen species (ROS), lignification and phytoalexins. The levels of some of the pathogenesis-related proteins were significantly higher upon Foc inoculation in the resistant plant. Interestingly, results also exhibited the crucial role of altered Yang cycle, which contributed in different methylation reactions and unfolded protein response in the chickpea roots against Foc. Overall, the observed modulations in the metabolic flux as outcome of several orchestrated molecular events are determinant of plant's role in chickpea-Foc interactions.

Influence of cadmium and mycorrhizal fungi on the fatty acid profile of flax (Linum usitatissimum) seeds

BACKGROUND

The soil environment can affect not only the quantity of crops produced but also their nutritional quality. We examined the combined effects of below-ground cadmium (0, 5, and 15 ppm) and mycorrhizal fungi (presence and absence) on the concentration of five major fatty acids within flax seeds (Linum usitatissimum).

RESULTS

Plants grown with mycorrhizal fungi produced seeds that contained higher concentrations of unsaturated (18:1, 18:2 and 18:3), but not saturated (16:0 and 18:0) fatty acids. The effects of mycorrhizal fungi on the concentration of unsaturated fatty acids in seeds were most pronounced when plant roots were exposed to 15 ppm Cd (i.e. the concentrations of 18:1, 18:2 and 18:3 increased by 169%, 370% and 150%, respectively).

CONCLUSIONS

The pronounced effects of mycorrhizal fungi on the concentration of unsaturated fatty acids at 15 ppm Cd may have been due to the presence of elevated levels of Cd within seeds. Our results suggest that, once the concentration of cadmium within seeds reaches a certain threshold, this heavy metal may improve the efficiency of enzymes that convert saturated fatty acids to unsaturated fatty acids.

Agriproteomics of Bread Wheat: Comparative Proteomics and Network Analyses of Grain Size Variation

Agriproteomics signifies the merging of agriculture research and proteomics systems science and is impacting plant research and societal development. Wheat is a frequently consumed foodstuff, has highly variable grain size that in effect contributes to wheat grain yield and the end-product quality. Very limited information is available on molecular basis of grain size due to complex multifactorial nature of this trait. Here, using liquid chromatography-mass spectrometry, we investigated the proteomics profiles from grains of wheat genotypes, Rye selection 111 (RS111) and Chinese spring (CS), which differ in their size. Significant differences in protein expression were found, including 33 proteins uniquely present in RS111 and 32 only in CS, while 54 proteins were expressed from both genotypes. Among differentially expressed proteins, 22 were upregulated, while 21 proteins were downregulated in RS111 compared to CS. Functional classification revealed their role in energy metabolism, seed storage, stress tolerance and transcription. Further, protein interactive network analysis was performed to predict the targets of identified proteins. Significantly different interactions patterns were observed between these genotypes with detection of proteins such as Cyp450, Sus2, and WRKY that could potentially affect seed size. The present study illustrates the potentials of agriproteomics as a veritable new frontier of plant omics research.

QTL for fatty acid composition and yield in linseed (Linum usitatissimum L.)

The combined SSR-SNP map and 20 QTL for agronomic and quality traits will assist in marker assisted breeding as well as map-based cloning of key genes in linseed. Flax is an important nutraceutical crop mostly because it is a rich source of omega-3 fatty acids and antioxidant compounds. Canada is the largest producer and exporter of oilseed flax (or linseed), creating a growing need to improve crop productivity and quality. In this study, a genetic map was constructed based on selected 329 single nucleotide polymorphic markers and 362 simple sequence repeat markers using a recombinant inbred line population of 243 individuals from a cross between the Canadian varieties CDC Bethune and Macbeth. The genetic map consisted of 15 linkage groups comprising 691 markers with an average marker density of one marker every 1.9 cM. A total of 20 quantitative trait loci (QTL) were identified corresponding to 14 traits. Three QTL each for oleic acid and stearic acid, two QTL each for linoleic acid and iodine value and one each for palmitic acid, linolenic acid, oil content, seed protein, cell wall, straw weight, thousand seed weight, seeds per boll, yield and days to maturity were identified. The QTL for cell wall, straw weight, seeds per boll, yield and days to maturity all co-located on linkage group 4. Analysis of the candidate gene regions underlying the QTL identified proteins involved in cell wall and fibre synthesis, fatty acid biosynthesis as well as their metabolism and yield component traits. This study provides the foundation for assisting in map-based cloning of the QTL and marker assisted selection of a wide range of quality and agronomic traits in linseed and potentially fibre flax.

Birth of plant proteomics in India: a new horizon

In the post-genomic era, proteomics is acknowledged as the next frontier for biological research. Although India has a long and distinguished tradition in protein research, the initiation of proteomics studies was a new horizon. Protein research witnessed enormous progress in protein separation, high-resolution refinements, biochemical identification of the proteins, protein-protein interaction, and structure-function analysis. Plant proteomics research, in India, began its journey on investigation of the proteome profiling, complexity analysis, protein trafficking, and biochemical modeling. The research article by Bhushan et al. in 2006 marked the birth of the plant proteomics research in India. Since then plant proteomics studies expanded progressively and are now being carried out in various institutions spread across the country. The compilation presented here seeks to trace the history of development in the area during the past decade based on publications till date. In this review, we emphasize on outcomes of the field providing prospects on proteomic pathway analyses. Finally, we discuss the connotation of strategies and the potential that would provide the framework of plant proteome research.

BIOLOGICAL SIGNIFICANCE

The past decades have seen rapidly growing number of sequenced plant genomes and associated genomic resources. To keep pace with this increasing body of data, India is in the provisional phase of proteomics research to develop a comparative hub for plant proteomes and protein families, but it requires a strong impetus from intellectuals, entrepreneurs, and government agencies. Here, we aim to provide an overview of past, present and future of Indian plant proteomics, which would serve as an evaluation platform for those seeking to incorporate proteomics into their research programs. This article is part of a Special Issue entitled: Proteomics in India.

Identification of multiple metabolic enzymes from mice cochleae tissue using a novel functional proteomics technology

A new type of technology in proteomics was developed in order to separate a complex protein mixture and analyze protein functions systematically. The technology combines the ability of two-dimensional gel electrophoresis (2-DE) to separate proteins with a protein elution plate (PEP) to recover active proteins for functional analysis and mass spectrometry (MS)-based identification. In order to demonstrate the feasibility of this functional proteomics approach, NADH and NADPH-dependent oxidases, major redox enzyme families, were identified from mice cochlear tissue after a specific drug treatment. By comparing the enzymatic activity between mice that were treated with a drug and a control group significant changes were observed. Using MS, five NADH-dependent oxidases were identified that showed highly altered enzymatic activities due to the drug treatment. In essence, the PEP technology allows for a systematic analysis of a large enzyme family from a complex proteome, providing insights in understanding the mechanism of drug treatment.

Dimethyl sulfide as a source of the seaweed-like aroma in cooked soybeans and correlation with its precursor, S-methylmethionine (vitamin U)

Among the soybean germplasm in Japan, two varieties, Nishiyamahitashi 98-5 (NH) and Shinanokurakake (SKK), have an intense seaweed-like flavor after cooking. Gas-liquid chromatography with mass spectrometry (GC-MS) indicated that a significant amount (11.5 ± 3.46 μg g(-1) for NH and 6.66 ± 0.91 μg g(-1) for SKK) of dimethyl sulfide (DMS) was formed after heat treatment. DMS is formed from S-methylmethionine (SMM, vitamin U). SMM was detected in all soybean varieties examined here, but its concentration in NH and SKK seeds was >100-fold higher than in the other varieties and ranged from 75 to 290 μg g(-1). The SMM content and the ability to form DMS upon heat treatment correlated among them. The plumes and radicles contained SMM exclusively. This is the first report of soybean varieties containing SMM at a level equivalent to or higher than that in vegetables known to contain high levels of SMM, for example, turnip, cabbage, and celery.

Radioactive Chernobyl environment has produced high-oil flax seeds that show proteome alterations related to carbon metabolism during seed development

Starting in 2007, we have grown soybean (Glycine max [L.] Merr. variety Soniachna) and flax (Linum usitatissimum, L. variety Kyivskyi) in the radio-contaminated Chernobyl area and analyzed the seed proteomes. In the second-generation flax seeds, we detected a 12% increase in oil content. To characterize the bases for this increase, seed development has been studied. Flax seeds were harvested in biological triplicate at 2, 4, and 6 weeks after flowering and at maturity from plants grown in nonradioactive and radio-contaminated plots in the Chernobyl area for two generations. Quantitative proteomic analyses based on 2-D gel electrophoresis (2-DE) allowed us to establish developmental profiles for 199 2-DE spots in both plots, out of which 79 were reliably identified by tandem mass spectrometry. The data suggest a statistically significant increased abundance of proteins associated with pyruvate biosynthesis via cytoplasmic glycolysis, L-malate decarboxylation, isocitrate dehydrogenation, and ethanol oxidation to acetaldehyde in early stages of seed development. This was followed by statistically significant increased abundance of ketoacyl-[acylcarrier protein] synthase I related to condensation of malonyl-ACP with elongating fatty acid chains. On the basis of these and previous data, we propose a preliminary model for plant adaptation to growth in a radio-contaminated environment. One aspect of the model suggests that changes in carbon assimilation and fatty acid biosynthesis are an integral part of plant adaptation.

PT-Flax (phenotyping and TILLinG of flax): development of a flax (Linum usitatissimum L.) mutant population and TILLinG platform for forward and reverse genetics

BACKGROUND

Flax (Linum usitatissimum L.) is an economically important fiber and oil crop that has been grown for thousands of years. The genome has been recently sequenced and transcriptomics are providing information on candidate genes potentially related to agronomically-important traits. In order to accelerate functional characterization of these genes we have generated a flax EMS mutant population that can be used as a TILLinG (Targeting Induced Local Lesions in Genomes) platform for forward and reverse genetics.

RESULTS

A population of 4,894 M2 mutant seed families was generated using 3 different EMS concentrations (0.3%, 0.6% and 0.75%) and used to produce M2 plants for subsequent phenotyping and DNA extraction. 10,839 viable M2 plants (4,033 families) were obtained and 1,552 families (38.5%) showed a visual developmental phenotype (stem size and diameter, plant architecture, flower-related). The majority of these families showed more than one phenotype. Mutant phenotype data are organised in a database and can be accessed and searched at UTILLdb (http://urgv.evry.inra.fr/UTILLdb). Preliminary screens were also performed for atypical fiber and seed phenotypes. Genomic DNA was extracted from 3,515 M2 families and eight-fold pooled for subsequent mutant detection by ENDO1 nuclease mis-match cleavage. In order to validate the collection for reverse genetics, DNA pools were screened for two genes coding enzymes of the lignin biosynthesis pathway: Coumarate-3-Hydroxylase (C3H) and Cinnamyl Alcohol Dehydrogenase (CAD). We identified 79 and 76 mutations in the C3H and CAD genes, respectively. The average mutation rate was calculated as 1/41 Kb giving rise to approximately 9,000 mutations per genome. Thirty-five out of the 52 flax cad mutant families containing missense or codon stop mutations showed the typical orange-brown xylem phenotype observed in CAD down-regulated/mutant plants in other species.

CONCLUSIONS

We have developed a flax mutant population that can be used as an efficient forward and reverse genetics tool. The collection has an extremely high mutation rate that enables the detection of large numbers of independant mutant families by screening a comparatively low number of M2 families. The population will prove to be a valuable resource for both fundamental research and the identification of agronomically-important genes for crop improvement in flax.