Ludovit Skultety

Comparative proteomic analysis of early-stage soybean seedlings responses to flooding by using gel and gel-free techniques.

Gel-based and gel-free proteomics techniques were used to investigate early responses to flooding stress in the roots and hypocotyls of soybean seedlings. Proteins from 2-day-old soybean seedlings flooded for 12 h were extracted and analyzed. Two mass-spectroscopy-based proteomics analyses, two-dimensional fluorescence difference gel electrophoresis, and nanoliquid chromatography identified 32 from 17 spots and 81 proteins, respectively, as responsive to flooding stress. On the basis of the number and function of proteins identified, glycolysis and fermentation enzymes and inducers of heat shock proteins were key elements in the early responses to flooding stress. Analysis of enzyme activities and carbohydrate contents in flooded seedlings showed that glucose degradation and sucrose accumulation accelerated during flooding due to activation of glycolysis and down-regulation of sucrose degrading enzymes. Additionally, the methylglyoxal pathway, which is detoxification system linked to glycolysis, was up-regulated. Furthermore, two-dimensional polyacrylamide gel electrophoresis-based phosphoproteomics analysis showed that proteins involved in protein folding and synthesis were dephosphorylated under flooding conditions. These results suggest that translational and post-translational control during flooding possibly induces an imbalance in the expression of proteins involved in several metabolic pathways including carbohydrate metabolism that might cause flooding injury of soybean seedlings.

Mass Spectrometry-Based Analysis of Proteomic Changes in the Root Tips of Flooded Soybean Seedlings

Flooding injury is a major problem in soybean cultivation. A proteomics approach was used to clarify the occurrence of changes in protein expression level and phosphorylation in soybeans under flooding stress. Two-day-old seedlings were flooded for 1 day, proteins were extracted from root tips of the seedlings and digested with trypsin, and their expression levels and phosphorylation states were compared to those of untreated controls using mass spectrometry-based proteomics techniques. Phosphoproteins were enriched using a phosphoprotein purification column prior to digestion and mass spectrometry. The expression of proteins involved in energy production increased as a result of flooding, while expression of proteins involved in protein folding and cell structure maintenance decreased. Flooding induced changes of phosphorylation status of proteins involved in energy generation, protein synthesis and cell structure maintenance. The response to flooding stress may be regulated by both modulation of protein expression and phosphorylation state. Energy-demanding and production-related metabolic pathways may be particularly subject to regulation by changes in protein phosphorylation during flooding.

Proteomic Analysis of Mature Soybean Seeds from the Chernobyl Area Suggests Plant Adaptation to the Contaminated Environment

The explosion in one of the four reactors of the Chernobyl Nuclear Power Plant (CNPP, Chernobyl) caused the worst nuclear environmental disaster ever seen. Currently, 23 years after the accident, the soil in the close vicinity of CNPP is still significantly contaminated with long-living radioisotopes, such as (137)Cs. Despite this contamination, the plants growing in Chernobyl area were able to adapt to the radioactivity, and survive. The aim of this study was to investigate plant adaptation mechanisms toward permanently increased level of radiation using a quantitative high-throughput proteomics approach. Soybeans of a local variety (Soniachna) were sown in contaminated and control fields in the Chernobyl region. Mature seeds were harvested and the extracted proteins were subjected to two-dimensional gel electrophoresis (2-DE). In total, 9.2% of 698 quantified protein spots on 2-D gel were found to be differentially expressed with a p-value </= 0.05. All differentially expressed spots were excised from the 2-D gels and analyzed by tandem mass spectrometry. Identified differentially expressed proteins were categorized into six main metabolic classes. Most abundant functional classes were associated with protein destination and storage followed by disease and defense. On the basis of the identity of these proteins, a working model for plant adaptation toward radio-contaminated Chernobyl soil conditions was proposed. Our results suggest that adaptation toward heavy metal stress, protection against radiation damage, and mobilization of seed storage proteins are involved in plant adaptation mechanism to radioactivity in the Chernobyl region.

Structural study on a lipopolysaccharide from Coxiella burnetii strain Nine Mile in avirulent phase II

A lipopolysaccharide isolated from Coxiella burnetti strain Nine Mile in avirulent phase II contains in the lipid A proximal region D-mannose, D-glycero-D-manno-heptose, and 3-deoxy-D- manno-oct-2-ulosonic acid (Kdo) in the molar ratio 2:2:3. The primary structure 1 of the heptasaccharide was determined by glycose analysis, methylation analysis, ESI-MS, and FABMS. [sequence: see text]

Detection and Identification of Coxiella burnetii Based on the Mass Spectrometric Analyses of the Extracted Proteins

Rapid and reliable detection, identification, and typing of bacterial species are necessary in response to natural or terrorist-caused outbreaks of infectious diseases and play crucial roles in diagnosis and efficient treatment. We report here two proteomic approaches with a high potential in the detection and identification of Coxiella burnetii, the causative agent of Q fever. The first of them starts with the acetonitrile (ACN) and trichloroacetic acid extractions of inactivated C. burnetii cells followed by the detection of extracted molecules and ions derived from the inactivated cells by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. In the second approach, identification of the proteins extracted by ACN is accomplished after enzymatic digestion by electrospray tandem mass spectrometry coupled to a nanoscale ultraperformance liquid chromatography (LC-MS/MS). In order to observe morphological differences on the surface structures upon extraction, the inactivated and treated cells of the bacterium were examined by electron microscopy. The LC-MS/MS approach has allowed identification of 20 proteins in the ACN extracts of C. burnetii strain RSA 493 that were observed in more than 3 out of 10 experiments.

NMR study of virenose and dihydrohydroxystreptose isolated from Coxiella burnetii phase I lipopolysaccharide

A lipopolysaccharide (LPS) isolated from Coxiella burnettii in virulent phase I contains in its O-polysaccharide chain two unusual sugars, virenose (6-deoxy-3-C-methylgulose) and dihydrohydroxystreptose [3-C-(hydroxymethyl)lyxose]. The sugars were isolated from LPS I, after acid hydrolysis and removal of lipid A, by a combination of HPLC and preparative paper chromatography. Their enantiomeric forms and ring conformations were established from optical rotation and NMR data. Two-dimensional COSY, HSQC, and HMBC as well as one- and two-dimensional NOEs were used to assign all proton and carbon signals in both monosaccharides. Virenose was found to be the D-gulo enantiomer with the 4C1 ring conformation and dihydrohydroxystreptose was shown to be the L-lyxo enantiomer also with the 4C1 conformation. The latter sugar was reported [S. Schramek, J. Radziejewska-Lebrecht, and H. Mayer, Eur. J. Biochem., 148 (1985) 455-461] to be present in LPS I in a furanose form, and it appears that a furanose to pyranose tautomerization took place in the course of the isolation procedure.

MSE Based Multiplex Protein Analysis Quantified Important Allergenic Proteins and Detected Relevant Peptides Carrying Known Epitopes in Wheat Grain Extracts

The amount of clinically relevant, allergy-related proteins in wheat grain is still largely unknown. The application of proteomics may create a platform not only for identification and characterization, but also for quantitation of these proteins. The aim of this study was to evaluate the data-independent quantitative mass spectrometry (MS(E)) approach in combination with 76 wheat allergenic sequences downloaded from the AllergenOnline database ( www.allergenonline.org ) as a starting point. Alcohol soluble extracts of gliadin and glutenin proteins were analyzed. This approach has resulted in identification and quantification of 15 allergenic protein isoforms that belong to amylase/trypsin inhibitors, γ-gliadins, and high or low molecular weight glutenins. Additionally, several peptides carrying four previously discovered epitopes of γ-gliadin B precursor have been detected. These data were validated against the UniProt database, which contained 11764 Triticeae protein sequences. The identified allergens are discussed in relation to Bakers asthma, food allergy, wheat dependent exercise induced anaphylaxis, atopic dermatitis, and celiac disease (i.e., gluten-sensitive enteropathy). In summary, the results showed that the MS(E) approach is suitable for quantitative analysis and allergens profiling in wheat varieties and/or other food matrices.

Proteomics analysis of flax grown in Chernobyl area suggests limited effect of contaminated environment on seed proteome.

The accident at the Chernobyl Nuclear Power Plant (CNPP) on April 26, 1986 is the most serious nuclear disaster in human history. Surprisingly, while the area proximal to the CNPP remains substantially contaminated with long-lived radioisotopes including (90)Sr and (137)Cs, the local ecosystem has been able to adapt. To evaluate plant adaptation, seeds of a local flax (Linum usitatissimum) variety Kyivskyi were sown in radio-contaminated and control fields of the Chernobyl region. A total protein fraction was isolated from mature seeds, and analyzed using 2-dimensional electrophoresis combined with tandem-mass spectrometry. Interestingly, growth of the plants in the radio-contaminated environment had little effect on proteome and only 35 protein spots differed in abundance (p-value of ≤0.05) out of 720 protein spots that were quantified for seeds harvested from both radio-contaminated and control fields. Of the 35 differentially abundant spots, 28 proteins were identified using state-of-the-art MS(E) method. Based on the observed changes, the proteome of seeds from plants grown in radio-contaminated soil display minor adjustments to multiple signaling pathways.

Coxiella burnetii Glycomics and Proteomics—Tools for Linking Structure to Function

Coxiella burnetii, the causative agent of Q fever, is an obligate intracellular bacterium and a highly infectious pathogen. The disease is a widespread zoonosis and is endemic throughout the world. An easy aerosol dissemination, environmental persistence, and high infectivity make the bacterium a serious threat for humans and animals. Lipopolysaccharide is considered one of the major factors of virulence expression and infection of the bacterium. Detailed glycomic studies enabled to better understand structural and functional peculiarities of this biopolymer and its role in pathogenesis and immunity of Q fever. Recent proteomic studies of C. burnetii have brought new approaches in accurate detection of the infectious agent and offered new insights into the inter‐ or intra‐species relatedness. Thus, structure/function relationship studies are currently of utmost importance in the field. This paper will focus on glycomic and proteomic approaches providing information on unique glycan and protein species of the microorganism as the candidate molecules for the use in detection/diagnosis, therapy, and prophylaxis.

Phase variation of Coxiella burneti0i strain Priscilla: influence of this phenomenon on biochemical features of its lipopolysaccharide

During the phase variation of Coxiella burnetii, modifications in its lipopolysaccharide (LPS) component were investigated. The cloned phase I C. burnetii cells were passed serially in chicken embryo yolk sacs up to the egg passage (EP) 90. The LPSs from the cells in EPs 3, 12, 21, 40, 60, and 90 were all separated by steric exclusion chromatography into three major populations: the high, intermediate, and low molecular weight fractions, differing one from another in size and chemical composition. No noticeable shortening of the O-polysaccharide chains was observed in the LPSs isolated during the C. burnetii cultivation. However, a redistribution of the existing LPS populations has been observed due to an increasing prevalence of those cells in the whole cell population that express LPS molecules with truncated O-chains and those being of R-type. In the high and intermediate molecular weight LPS populations, virenose and dihydrohydroxystreptose are lost gradually with the progress in phase variation. This occurs more readily with the former sugar. At present, the molecular mechanisms influencing the LPS modifications during the C. burnetii phase variation remain unclear.