Mass Spectrometry-Based Proteomic Approach in Oenococcus oeni Enological Starter

On-Line Thermally Induced Evolved Gas Analysis: An Update-Part 1: EGA-MS

Advances in on-line thermally induced evolved gas analysis (OLTI-EGA) have been systematically reported by our group to update their applications in several different fields and to provide useful starting references. The importance of an accurate interpretation of the thermally-induced reaction mechanism which involves the formation of gaseous species is necessary to obtain the characterization of the evolved products. In this review, applications of Evolved Gas Analysis (EGA) performed by on-line coupling heating devices to mass spectrometry (EGA-MS), are reported. Reported references clearly demonstrate that the characterization of the nature of volatile products released by a substance subjected to a controlled temperature program allows us to prove a supposed reaction or composition, either under isothermal or under heating conditions. Selected 2019, 2020, and 2021 references are collected and briefly described in this review.

Analytical Strategy for MS-Based Thanatochemistry to Estimate Postmortem Interval

An analytical strategy for a matrix-assisted laser desorption mass spectrometry-based untargeted metabolomic study on vitreous humor (VH) was developed, looking for statistically significant parameters correlated to death time estimation. Five incubation stages of VH, 0, 24, 48, 72, and 96 h, at physiological pH and controlled temperature, were adopted to monitor time-dependent changes and correlate them with the postmortem interval (PMI). Using two multivariate statistical approaches, principal component regression (PCR) and partial least squares regression (PLSR), the PMI was assessed, considering the m/z values from mass spectra and the incubation time (ISt) as predictors. An independent validation set was used to evaluate the predictive capability of the models through the coefficient of determination (R²) and the root-mean-square error (RMSE). Different pre-treatments were applied to the raw mass spectra, and their performance in assessing PMI was evaluated. Based on the best outcomes in terms of both R² and RMSE, multiplicative scatter correction combined with a logarithmic transformation was chosen. The results of PCR and PLSR based on the selected pre-treatment are encouraging because validation R² is about 0.95 for both models. Moreover, the prediction error is 6 h for both models, when PMI is lower than 1 day. Although these results are obtained by the uncritical application of the models, they are comparable to or even better than those reported in the literature. Notwithstanding, we consider that many in situ influences, such as passive diffusion, functional loss of tissues, and advanced autolytic processes, could not get captured in vitro. However, the developed approach was optimized using VH samples and overcomes the limitations of the vast majority of methods that require validation for serum and/or urine samples.

The mitochondrial aspartate/glutamate carrier (AGC or Aralar1) isoforms in D. melanogaster: biochemical characterization, gene structure, and evolutionary analysis

BACKGROUND

In man two mitochondrial aspartate/glutamate carrier (AGC) isoforms, known as aralar and citrin, are required to accomplish several metabolic pathways. In order to fill the existing gap of knowledge in Drosophila melanogaster, we have studied aralar1 gene, orthologue of human AGC-encoding genes in this organism.

METHODS

The blastp algorithm and the "reciprocal best hit" approach have been used to identify the human orthologue of AGCs in Drosophilidae and non-Drosophilidae. Aralar1 proteins have been overexpressed in Escherichia coli and functionally reconstituted into liposomes for transport assays.

RESULTS

The transcriptional organization of aralar1 comprises six isoforms, three constitutively expressed (aralar1-RA, RD and RF), and the remaining three distributed during the development or in different tissues (aralar1-RB, RC and RE). Aralar1-PA and Aralar1-PE, representative of all isoforms, have been biochemically characterized. Recombinant Aralar1-PA and Aralar1-PE proteins share similar efficiency to exchange glutamate against aspartate, and same substrate affinities than the human isoforms. Interestingly, although Aralar1-PA and Aralar1-PE diverge only in their EF-hand 8, they greatly differ in their specific activities and substrate specificity.

CONCLUSIONS

The tight regulation of aralar1 transcripts expression and the high request of aspartate and glutamate during early embryogenesis suggest a crucial role of Aralar1 in this Drosophila developmental stage. Furthermore, biochemical characterization and calcium sensitivity have identified Aralar1-PA and Aralar1-PE as the human aralar and citrin counterparts, respectively.

GENERAL SIGNIFICANCE

The functional characterization of the fruit fly mitochondrial AGC transporter represents a crucial step toward a complete understanding of the metabolic events acting during early embryogenesis.

Complexation of As(III) by phosphonate ligands in aqueous fluids: Thermodynamic behavior, chemical binding forms and sequestering abilities

In recent years, the contamination of water by arsenic reached alarming levels in many countries of the world, attracting the interest of many researchers engaged in testing methodologies able to remove this harmful pollutant. An important aspect that must be taken into consideration is the possibility to find arsenic in different chemical forms which could require different approaches for its removal. At this aim, a speciation analysis appears to be crucial for better understanding the behavior of arsenic species in aqueous solutions, especially in presence of compounds with marked chelating properties. Phosphonates can be identified as good sequestering agents and, at this purpose, this manuscript intends to investigate the interaction of As(III) with three phosphonic acids derived from nitrilotriacetic acid (NTA) by replacements of one (N-(Phosphonomethyl) iminodiacetic acid, NTAP), two (N,N-Bis-(phosphonomethyl) glycine, NTA2P) and three (Nitrilotri(methylphosphonic acid), NTA3P) carboxylic groups with the same number of phosphonate groups. An in-depth potentiometric and calorimetric investigation allowed to determine speciation models featured by simple ML, MLH_i and ML(OH) species. A complete thermodynamic characterization of the systems is reported together with the definition of coordination mode by mass spectrometry measurements. On the light of the speciation models, the possibility of using these ligands in arsenic removal techniques was assessed by determining the pL_0.5 (the concentration of ligand able to remove the 50% of metal ion present in trace). All ligands show a good sequestering ability, in particular under the conditions of fresh water, following the trend NTA3P > NTA2P > NTAP.

An Innovative Multilevel Test for Hemoglobinopathies: TGA/Chemometrics Simultaneously Identifies and Classifies Sickle Cell Disease From Thalassemia

Introduction: Hemoglobinopathies are the most common genetic disorder wordlwide and because of migrations are become an emerging global health problem. Screening programmes for Sickle cell disease and Thalassemia have been implemented in some countries, but are not a common practice, due to a lack in the accuracy of the methods and to the costs of the analyses. Objectives: The objective of this study was the application of the thermogravimetry coupled to chemometrics as new screening method to perform an early diagnosis of thalassemia and sickle cell disease. Methods: Whole blood samples (30 μL) from sickle cell anemia and thalassemia patients were analyzed using the thermobalance TG7 and the resulting curves were compared with those of healthy individuals. A chemometric approach based on Principal Components Analysis (PCA) was exploited to enhance correlation between thermogravimetric profiles and a model of prediction by Partial Least Square Discriminant Analysis (PLS-DA) was developed and validated. Results: The characteristic profile of the blood sample thermal decomposition and the first derivative of the TG curve showed that patients were clearly distinguished from healthy individuals as a result of different amounts of water and corpuscular fraction of blood. The chemometric approach based on PCA allowed a quick identification of differences between healthy subjects and patients and also between thalassemic and sickle cell anemia subjects. Chemometric tools (PLS-DA) were used to validate a model of prediction to process the thermogravimetric curves and to obtain in 1 h an accurate diagnosis. The TGA/Chemometric test permitted to perform first level test for hemoglobinopathies with the same accuracy of confirmatory analyses obtained by the molecular investigation. Conclusions: A screening test based on the coupling of thermogravimetry and chemometrics was optimized for the differential diagnosis of hemoglobinopathies. The novel test is able to simultaneously perform a simple and fast diagnosis of sickle cell anemia or thalassemia, in a single analysis of few microliters of non-pretreated whole blood at low cost, and with high accuracy. Moreover this method results particularly suitable in pediatric patients as it requires small sample volumes and is able to characterize also transfused patients.

Protein Extraction, Enrichment and MALDI MS and MS/MS Analysis from Bitter Orange Leaves (Citrus aurantium)

Citrus aurantium is a widespread tree in the Mediterranean area, and it is mainly used as rootstock for other citrus. In the present study, a vacuum infiltration centrifugation procedure, followed by solid phase extraction matrix-assisted laser desorption ionization tandem mass spectrometry (SPE MALDI MS/MS) analysis, was adopted to isolate proteins from leaves. The results of mass spectrometry (MS) profiling, combined with the top-down proteomics approach, allowed the identification of 78 proteins. The bioinformatic databases TargetP, SignalP, ChloroP, WallProtDB, and mGOASVM-Loc were used to predict the subcellular localization of the identified proteins. Among 78 identified proteins, 20 were targeted as secretory pathway proteins and 36 were predicted to be in cellular compartments including cytoplasm, nucleus, and cell membrane. The largest subcellular fraction was the secretory pathway, accounting for 25% of total proteins. Gene Ontology (GO) of Citrus sinensis was used to simplify the functional annotation of the proteins that were identified in the leaves. The Kyoto Encyclopedia of Genes and Genomes (KEGG) showed the enrichment of metabolic pathways including glutathione metabolism and biosynthesis of secondary metabolites, suggesting that the response to a range of environmental factors is the key processes in citrus leaves. Finally, the Lipase GDSL domain-containing protein GDSL esterase/lipase, which is involved in plant development and defense response, was for the first time identified and characterized in Citrus aurantium.

MS-based proteomic analysis of cardiac response to hypoxia in the goldfish (Carassius auratus)

The exceptional hypoxia tolerance of the goldfish heart may be achieved through the activation of an alternative mechanism recruiting the first product of the anaerobic glycolysis (i.e. piruvate). This hypothesis led to design a classical mass spectrometry based proteomic study to identify in the goldfish cardiac proteins that may be associated with maintaining heart function under normoxia and hypoxia. A selective protein solubilization, SDS PAGE, trypsin digestion and MALDI MS/MS analysis allowed the identification of the 12 most stable hypoxia-regulated proteins. Among these proteins, five are enzymes catalyzing reversible steps of the glycolysis/gluconeogenesis network. Protein composition reveals the presence of fructose-1,6-bisphosphate aldolase B as a specific hypoxia-regulated protein. This work indicated that the key enzyme of reversible steps of the glycolysis/gluconeogenesis network is fructose-1,6-bisphosphate, aldolase B, suggesting a role of gluconeogenesis in the mechanisms involved in the goldfish heart response to hypoxia.

Identification of Hanks-Type Kinase PknB-Specific Targets in the Streptococcus thermophilus Phosphoproteome

Protein phosphorylation especially on serine/threonine/tyrosine residues are frequent in many bacteria. This post-translational modification has been associated with pathogenicity and virulence in various species. However, only few data have been produced so far on generally recognized as safe bacteria used in food fermentations. A family of kinases known as Hanks-type kinases is suspected to be responsible for, at least, a part of these phosphorylations in eukaryotes as in bacteria. The objective of our work was to establish the first phosphoproteome of Streptococcus thermophilus, a lactic acid bacterium widely used in dairy fermentations in order to identified the proteins and pathways tagged by Ser/Thr/Tyr phosphorylations. In addition, we have evaluated the role in this process of the only Hanks-type kinase encoded in the S. thermophilus genome. We have constructed a mutant defective for the Hanks type kinase in S. thermophilus and established the proteomes and phosphoproteomes of the wild type and the mutant strains. To do that, we have enriched our samples in phosphopeptides with titane beads and used dimethyl tags to compare phosphopeptide abundances. Peptides and phosphopeptides were analyzed on a last generation LC-MS/MS system. We have identified and quantified 891 proteins representing half of the theoretical proteome. Among these proteins, 106 contained phosphorylated peptides. Various functional groups of proteins (amino acid, carbon and nucleotide metabolism, translation, cell cycle, stress response, …) were found phosphorylated. The phosphoproteome was only weakly reduced in the Hanks-type kinase mutant indicating that this enzyme is only one of the players in the phosphorylation process. The proteins that are modified by the Hanks-type kinase mainly belong to the divisome.

Molecular species fingerprinting and quantitative analysis of saffron (Crocus sativus L.) for quality control by MALDI mass spectrometry

Herein we describe a rapid, simple, and reliable method for the quantitative analysis and molecular species fingerprinting of saffron (Crocus sativus L.) by direct MS and MS/MS analysis. Experimentally, powdered saffron was subjected to a brief treatment with a 0.3% TFA water/acetonitrile solution, and the resulting mixture was directly placed on the MALDI plate for analysis. This approach allowed the detection of the commonly observed crocins C-1-C-6 and flavonols, together with the identification of the unknown highly glycosylated crocins C-7, C-8 and C-9, and carotenoid-derived metabolites. The strategy endorsed the simultaneous detection and characterization of saffron and adulterant markers using crude extracts of the adulterant itself and synthetic sets of adulterated authentic saffron samples. The implementation of the strategy was to measure the amount of an unknown adulterant from the crude extract using curcumin as a non-isotopic isobaric internal standard. The relationship between the saffron and curcumin molar ratios were established with a correlation coefficient of 0.9942. The ANOVA regression model was significant, F(1, 72) = 13 595.82, p < 0.001, y = (0.0116 ± 0.0001)x + (-0.1214 ± 0.0086). No matrix effects were observed and good results were obtained with respect to instrumental repeatability (*RSD% < 2%) and LOD (1.1%). The analysis of commercial samples of saffron using the proposed approach showed the suitability of the method for routine analysis (minimal sample preparation and very short measuring time per sample).

Human coelomic fluid investigation: A MS-based analytical approach to prenatal screening

Coelomic fluid (CF) is the earliest dynamic and complex fluid of the gestational sac. CF contains maternal cells and proteins produced by embryonic cells, tissues and excretions. The biochemical composition of CF is modified throughout the first trimester of pregnancy and its protein profile reflects both physiological/pathological changes affecting the embryo and mother. Identification of variations in the balance of proteins might indicate particular types of pathologies, or ascertain specific genetic disorders. A platform utilizing protein enrichment procedures coupled with shotgun identification and iTRAQ differentiation provided the identification and quantitation of 88 unique embryonic proteins. It is relevant to note that chromosome X protein CXorf23 was found suggesting the embryo sex. Foetal sex was determined by Quantitative Fluorescent Polymerase Chain Reaction (QF-PCR) on coelomic cells, foetal tissues and maternal white blood cells, with a 100% concordance rate between iTRAQ-MS/MS and QF-PCR data. The functional associations among the identified proteins were investigated using STRING database. Open Targets Platform showed as significant the following therapeutic areas: nervous, respiratory, eye and head system disease.

Ethanol stress in Oenococcus oeni: transcriptional response and complex physiological mechanisms

Oenococcus oeni is the dominant species able to cope with a hostile environment of wines, comprising cumulative effects of low pH, high ethanol and SO₂ content, nonoptimal growth temperatures and growth inhibitory compounds. Ethanol tolerance is a crucial feature for the activity of O. oeni cells in wine because ethanol acts as a disordering agent of its cell membrane and negatively affects metabolic activity; it damages the membrane integrity, decreases cell viability and, as other stress conditions, delays the start of malolactic fermentation with a consequent alteration of wine quality. The cell wall, cytoplasmic membrane and metabolic pathways are the main sites involved in physiological changes aimed to ensure an adequate adaptive response to ethanol stress and to face the oxidative damage caused by increasing production of reactive oxygen species. Improving our understanding of the cellular impact of ethanol toxicity and how the cell responds to ethanol stress can facilitate the development of strategies to enhance microbial ethanol tolerance; this allows to perform a multidisciplinary endeavour requiring not only an ecological study of the spontaneous process but also the characterization of useful technological and physiological features of the predominant strains in order to select those with the highest potential for industrial applications.

Mass spectrometry and potentiometry studies of Al(iii)–naringin complexes

Here we have studied the complexation of naringin with Al(iii) under physiological conditions (i.e., at 37 °C and in 0.16 mol L⁻¹NaCl).

Transcriptomic and Proteomic Analysis of Oenococcus oeni Adaptation to Wine Stress Conditions

Oenococcus oeni, the main lactic acid bacteria responsible for malolactic fermentation in wine, has to adapt to stressful conditions, such as low pH and high ethanol content. In this study, the changes in the transcriptome and the proteome of O. oeni PSU-1 during the adaptation period before MLF start have been studied. DNA microarrays were used for the transcriptomic analysis and two complementary proteomic techniques, 2-D DIGE and iTRAQ labeling were used to analyze the proteomic response. One of the most influenced functions in PSU-1 due to inoculation into wine-like medium (WLM) was translation, showing the over-expression of certain ribosomal genes and the corresponding proteins. Amino acid metabolism and transport was also altered and several peptidases were up regulated both at gene and protein level. Certain proteins involved in glutamine and glutamate metabolism showed an increased abundance revealing the key role of nitrogen uptake under stressful conditions. A strong transcriptional inhibition of carbohydrate metabolism related genes was observed. On the other hand, the transcriptional up-regulation of malate transport and citrate consumption was indicative of the use of L-malate and citrate associated to stress response and as an alternative energy source to sugar metabolism. Regarding the stress mechanisms, our results support the relevance of the thioredoxin and glutathione systems in the adaptation of O. oeni to wine related stress. Genes and proteins related to cell wall showed also significant changes indicating the relevance of the cell envelop as protective barrier to environmental stress. The differences found between transcriptomic and proteomic data suggested the relevance of post-transcriptional mechanisms and the complexity of the stress response in O. oeni adaptation. Further research should deepen into the metabolisms mostly altered due to wine conditions to elucidate the role of each mechanism in the O. oeni ability to develop MLF.

Targeted proteomic approach in prostatic tissue: a panel of potential biomarkers for cancer detection

Prostate cancer (PCa) is the sixth highest causes of cancer-related deaths in men. The molecular events underlying its behavior and evolution are not completely understood. Prostate-specific antigen (PSA) is the only approved Food and Drug Administration biomarker. A panel of ten stage-specific tumoral and adjacent non tumoral tissues from patients affected by PCa (Gleason score 6, 3+3; PSA 10 ÷19 ng/ml) was investigated by MS-based proteomics approach. The proposed method was based on identifying the base-soluble proteins from tissue, established an efficient study, which lead to a deeper molecular perspective understanding of the PCa. A total of 164 proteins were found and 132 of these were evaluated differentially expressed in tumoral tissues. The Ingenuity Pathway Analysis (IPA) showed that among all dataset obtained, 105 molecules were involved in epithelial neoplasia with a p-value of 3.62E-05, whereas, only 11 molecules detected were ascribed to sentinel tissue and bodily fluids.

A major allergen in rainbow trout (Oncorhynchus mykiss): complete sequences of parvalbumin by MALDI tandem mass spectrometry

Fish parvalbumin (PRVB) is an abundant and stable protein in fish meat. The variation in cross-reactivity among individuals is well known and explained by a broad repertoire of molecular forms and differences between IgE-binding epitopes in fish species. PVRB has "sequential" epitopes, which retain their IgE-binding capacity and allergenicity also after heating and digestion using proteolytic enzymes. From the allergonomics perspective, PRVB is still a challenging target due to its multiple isoforms present at different degrees of distribution. Little information is available in the databases about PVRBs from Oncorhynchus mykiss. At present, only two validated, incomplete isoforms of this species are included in the protein databases: parvalbumin beta 1 (P86431) and parvalbumin beta 2 (P86432). A simple and rapid protocol has been developed for selective solubilization of PRVB from the muscle of farmed rainbow trout (Oncorhynchus mykiss), followed by calcium depletion, proteolytic digestion, MALDI MS, and MS/MS analysis. With this strategy thermal allergen release was assessed and PRVB1 (P86431), PRVB1.1, PRVB2 (P86432) and PRVB2.1 variants from the rainbow trout were sequenced. The correct ordering of peptide sequences was aided by mapping the overlapping enzymatic digests. The deduced peptide sequences were arranged and the theoretical molecular masses (Mr) of the resulting sequences were calculated. Experimental masses (Mr) of each PRVB variant were measured by linear MALDI-TOF.

Determination of ketosteroid hormones in meat by liquid chromatography tandem mass spectrometry and derivatization chemistry

A method for the determination and quantification of ketosteroid hormones in meat by mass spectrometry, based on the derivatization of the carbonyl moiety of steroids by O-methylhydroxylamine, is presented. The quantitative assay is performed by means of multiple-reaction-monitoring (MRM) scan mode and using the corresponding labelled species, obtained by reaction with d 3-methoxylamine, as internal standard. The accuracy of the method was established by evaluating artificially spiked samples, obtaining values in the range 90-110%. Recovery tests were performed on blank matrix samples spiked with non-natural steroids including trenbolone and melengestrol acetate. The latter experiment revealed that the yield of the extraction processes was approximately 60%. Good values of LOQ and LOD were achieved, making this method competitive with current hormone assay methods.