Proteomic and metabolic profiles of Cakile maritima Scop. Sea Rocket grown in the presence of cadmium.

Recent physiological reports have documented how Cakile maritima Scop. Sea Rocket could accumulate high doses of Cd without altering its physiological parameters. In the present study, we performed an integrated proteomics (2DE) and metabolomics (HPLC-MS) investigation to determine the molecular mechanisms underlying cadmium (Cd) tolerance of this halophyte. Peculiar features were observed: (i) up-regulation of thiol compound anabolism, including glutathione and phytochelatin homeostasis, which allows an intracellular chelation of Cd and its compartmentalization into vacuole by a significant up-regulation of vacuolar transporters; (ii) up-regulation of the PPP and Calvin cycle (both at the enzyme and metabolite level), which utterly promoted the maintenance of NADPH/NADP(+) homeostasis, other than the accumulation of triose-phosphates (serving as anabolic intermediates for triacylglycerol biosynthesis) and the glyoxylate precursor phosphoglycolate, to promote photorespiration and consequently CO2 release. An up-regulation of carbonic anhydrase was also observed. This halophyte is also correlated with a highly efficient antioxidant system, especially a high up-regulation of SOD1, resulting more efficient in coping with heavy metals stress than common plants. Interestingly, exposure to high Cd concentrations partly affected photosystem integrity and metabolic activity, through the up-regulation of enzymes from the Calvin cycle and glutathione-ascorbate homeostasis and PAP3 which stabilizes thylakoid membrane structures. In addition, up-regulation of Peptidyl-prolyl isomerase CYP38 increases stability and biogenesis of PSII. Finally, metabolomics results confirmed proteomics and previous physiological evidence, also suggesting that osmoprotectants, betaine and proline, together with plant hormones, methyl jasmonate and salicylic acid, might be involved in mediating responses to Cd-induced stress. Taken together, these peculiar features confirm that Cakile maritima Scop. Sea Rocket seemed to be naturally equipped to withstand even high doses of Cd pollution.

Thiol-based regulation of glyceraldehyde-3-phosphate dehydrogenase in blood bank-stored red blood cells: a strategy to counteract oxidative stress.

BACKGROUND: Red blood cell (RBC) glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a glycolytic enzyme normally inhibited upon binding to the membrane-spanning protein Band 3, but active when free in the cytosol. Accumulating evidence in other cells indicates that oxidative thiol modifications in cytosolic GAPDH drive this molecule into functional avenues that deviate from glycolysis. This study aimed to investigate the role of GAPDH in oxidative stress-dependent metabolic modulations occurring in SAGM-stored RBCs, to increase the knowledge of the molecular mechanisms affecting RBC survival and viability under blood banking conditions. STUDY DESIGN AND METHODS: Membranes and cytosol from CPD SAGM-stored RBCs were subjected to Western blotting with anti-GAPDH at 0, 7, 14, 21, 28, 35, and 42 days of preservation. Immunoreactive bands were excised, digested with trypsin, and analyzed by mass spectrometry for the presence of oxidative posttranslational modifications. GAPDH enzymatic activity was also measured in the cytosolic fraction during storage. RESULTS: At 21 days of storage, we demonstrated that cytosolic GAPDH undergoes temporary inactivation due to the formation of an intramolecular disulfide bond between the active-site Cys-152 and nearby Cys-156, a mechanism to rerouting glucose flux toward the pentose phosphate pathway. In addition, an increase in the membrane-bound GAPDH was detected in long-stored RBCs. CONCLUSION: Reversible inhibition or activation of cytosolic GAPDH may represent a protective strategy against oxidative stress to favor NADPH production in stored RBCs.

Analysis of TAp73-dependent signaling via omics technologies.

Transactivation-proficient (TA) p73 is a transcription factor belonging to the p53 family, which regulates a variety of biological processes, including neurogenesis, differentiation, apoptosis, and DNA damage checkpoint response. In the present study, we adopted multiple Omics approaches, based upon the simultaneous application of metabolomics, lipidomics, and proteomics, in order to dissect the intracellular pathways activated by p73. As cellular model, we utilized a clone of the human osteosarcoma SAOS-2 cell line that allows the expression of TAp73α in an inducible manner. We found that TAp73α promoted mitochondrial activity (accumulation of metabolic intermediates and up-regulation of proteins related to the Krebs cycle), boosted glutathione homeostasis, increased arginine-citrulline-NO metabolism, altered purine synthesis, and promoted the pentose phosphate pathway toward NADPH accumulation for reducing and biosynthetic purposes. Indeed, lipid metabolism was driven toward the accumulation and oxidation of long-chain fatty acids with pro-apoptotic potential. In parallel, the expression of TAp73α was accompanied by the dephosphorylation of key proteins of the mitotic spindle assembly checkpoint. In conclusion, the obtained results confirm existing evidence from transcriptomics analyses and suggest a role for TAp73α in the regulation of cellular metabolism, cell survival, and cell growth.

Proteomic analysis of platelets treated with gamma irradiation versus a commercial photochemical pathogen reduction technology.

BACKGROUND: Several strategies are currently being tested to reduce the risk of pathogen transmission associated with platelet (PLT) transfusion. Within the framework of the Italian Platelet Technology Assessment Study, we investigated the variations of the protein profiles (proteomics) of apheresis PLT concentrates (PCs) upon treatment with riboflavin and ultraviolet (UV) light (Mirasol; 6.24 J/mL; 280-400 nm). STUDY DESIGN AND METHODS: Control, gamma-irradiated, and Mirasol-treated apheresis PCs were assayed on Days 1 and 5 of storage by means of gel-based analytical approaches (two-dimensional gel electrophoresis) and mass spectrometry-based identification of significant (p < 0.05 analysis of variance) differential proteins. Supernatants were then assayed for metabolism and oxidative stress-related metabolites through multiple reaction monitoring mass spectrometry. RESULTS: Only a handful of modifications could be observed in the PLT proteome profiles in response to the Mirasol treatment, which included proteins involved in oxidative stress responses, PLT metabolism, and activation. Results confirmed increased metabolic rate and oxidative stress in the supernatants of treated PLTs (both gamma irradiated and Mirasol treated). CONCLUSION: From this investigation, it emerges that, from a proteomics standpoint, gamma irradiation results in the acceleration of PLT storage lesions and the Mirasol treatment only moderately exacerbates these phenomena.

Red blood cell subpopulations in freshly drawn blood: application of proteomics and metabolomics to a decades-long biological issue.

BACKGROUND: It has long been known that red blood cells comprise various subpopulations, which can be separated through Percoll density gradients. MATERIALS AND METHODS: In this study, we performed integrated flow cytometry, proteomic and metabolomic analyses on five distinct red blood cell subpopulations obtained by Percoll density gradient separation of freshly drawn leucocyte-depleted erythrocyte concentrates. The relation of density gradient fractions to cell age was confirmed through band 4.1a/4.1b assays. RESULTS: We observed a decrease in size and increase in cell rugosity in older (denser) populations. Metabolomic analysis of fraction 5 (the oldest population) showed a decrease of glycolytic metabolism and of anti-oxidant defence-related mechanisms, resulting in decreased activation of the pentose phosphate pathway, less accumulation of NADPH and reduced glutathione and increased levels of oxidized glutathione. These observations strengthen conclusions about the role of oxidative stress in erythrocyte ageing in vivo, in analogy with results of recent in vitro studies. On the other hand, no substantial proteomic differences were observed among fractions. This result was partly explained by intrinsic technical limitations of the two-dimensional gel electrophoresis approach and the probable clearance from the bloodstream of erythrocytes with membrane protein alterations. Since this clearance effect is not present in vitro (in blood bank conditions), proteomic studies have shown substantial membrane lesions in ageing red blood cells in vitro. CONCLUSION: This analysis shows that the three main red blood cell subpopulations, accounting for over 92% of the total RBC, are rather homogeneous soon after withdrawal. Major age-related alterations in vivo probably affect enzyme activities through post-translational mechanisms rather than through changes in the overall proteomic profile of RBC.

Red blood cell populations and membrane levels of peroxiredoxin 2 as candidate biomarkers to reveal blood doping.

BACKGROUND: Blood doping represents one main trend in doping strategies. Blood doping refers to the practice of boosting the number of red blood cells (RBCs) in the bloodstream in order to enhance athletic performance, by means of blood transfusions, administration of erythropoiesis-stimulating substances, blood substitutes, natural or artificial altitude facilities, and innovative gene therapies. While detection of recombinant EPO and homologous transfusion is already feasible through electrophoretic, mass spectrometry or flow cytometry-based approaches, no method is currently available to tackle doping strategies relying on autologous transfusions. MATERIALS AND METHODS: We exploited an in vitro model of autologous transfusion through a 1:10 dilution of concentrated RBCs after 30 days of storage upon appropriate dilution in freshly withdrawn RBCs from the same donor. Western blot towards membrane Prdx2 and Percoll density gradients were exploited to assess their suitability as biomarkers of transfusion. RESULTS: Membrane Prdx2 was visible in day 30 samples albeit not in day 0, while it was still visible in the 1:10 dilution of day 30 in day 0 RBCs. Cell gradients also highlighted changes in the profile of the RBC subpopulations upon dilution of stored RBCs in the fresh ones. DISCUSSION: From this preliminary in vitro investigation it emerges that Prdx2 and RBC populations might be further tested as candidate biomarkers of blood doping through autologous transfusion, though it is yet to be assessed whether the kinetics in vivo of Prdx2 exposure in the membrane of transfused RBCs will endow a sufficient time-window to allow reliable anti-doping testing.

Chianina beef tenderness investigated through integrated Omics.

In the present study we performed an integrated proteomics, interactomics and metabolomics analysis of Longissimus dorsi tender and tough meat samples from Chianina beef cattle. Results were statistically handled as to obtain Pearson's correlation coefficients of the results from Omics investigation in relation to canonical tenderness-related parameters, including Warner Bratzler shear force, myofibrillar degradation (at 48 h and 10 days after slaughter), sarcomere length and total collagen content. As a result, we could observe that the tender meat group was characterized by higher levels of glycolytic enzymes, which were over-phosphorylated and produced accumulation of glycolytic intermediates. Oxidative stress promoted meat tenderness and elicited heat shock protein responses, which in turn triggered apoptosis-like cascades along with PARP fragmentation. Phosphorylation was found to be a key process in post mortem muscle conversion to meat, as it was shown not only to modulate glycolytic enzyme activities, but also mediate the stability of structural proteins at the Z-disk. On the other hand, phosphorylation of HSPs has been supposed to alter their functions through changing their affinity for target interactors. Analogies and breed-specific differences are highlighted throughout the text via a direct comparison of the present results against the ones obtained in a parallel study on Maremmana Longissimus dorsi. It emerges that, while the main cornerstones and the final outcome are maintained, post mortem metabolism in tender and tough meat yielding individuals is subtly modulated via specific higher levels of enzymes and amino acidic residue phosphorylation in a breed-specific fashion, and whether calcium homeostasis dysregulation was a key factor in Maremmana, higher early post mortem phosphocreatine levels in the Chianina tender group could favor a slower and prolonged glycolytic rate, prolonging the extent of the minimum hanging period necessary to obtain tender meat from this breed by a few days.

Love me tender: an Omics window on the bovine meat tenderness network.

Meat tenderness prediction is a challenging task, especially in Maremmana, an Italian autochtonous and highly appreciated beef breed. In the present study we reported an integrated proteomics, phosphoproteomics and metabolomics overview of meat tenderness in longissimus dorsi from 15 male Maremmana individuals, through the discrimination of tender and tough groups via standard meat tenderness indicators (WBS, MFI(4 h), MFI(10 days), sarcomere length) and their correlation with results from Omics analyses. Results revealed that the tender meat group was characterized by higher levels of glycolytic enzymes, which were less phosphorylated and overall more active (lactate accumulation was higher in the tender group), than in tough counterparts. Additionally, we could observe a higher level of oxidative stress in the tender group. No proteomics nor phosphoproteomics result hinted at the widely accepted role of calpains and cathepsins, except for the indication of calcium homeostasis dysregulation. Nevertheless, myofibrillar degradation was monitored and related to structural protein fragmentations. Fragmentation of structural proteins and activities of glycolytic enzymes were inversely related to their phosphorylation levels, suggesting that PTMs might add further levels of complexity in the frame of meat tenderness.

Meat quality of the longissimus lumborum muscle of Casertana and Large White pigs: metabolomics and proteomics intertwined.

Longissimus lumborum muscles from high fat-deposing Casertana and lean meat Large White pigs were assayed for meat quality parameters, including early and ultimate post mortem pH, water holding capacity and Minolta L*a*b*values. These parameters were correlated to results from differential proteomic and targeted metabolomic analyses. Higher levels of glycolytic enzymes and lactate accumulation were related to slow pH drop in Casertana pigs, albeit not to rapid pH lowering in LW counterparts. On the other hand, the individuation of pyruvate kinaseM1 and tropomyosin levels in LW were related to water holding capacity and Minolta values at 24h after slaughter. Bioinformatic analyses strengthened the correlation between over-expression of structural proteins in LW and more accentuated growth aptitude in this breed. Conversely, enzymes taking part into branching glycolytic reactions, such as glycerol 3-phosphate and creatine kinase M, were related to accentuated lipogenesis and slower albeit prolonged glycolytic rate in Casertana, respectively. Breed-specific differences at the protein level were not only related to growth performances and fat accumulation tendency in vivo, but they also affected post mortem performances through a direct influence on the forcedly anaerobic behavior of pig muscles after slaughter.

Proteomic analysis of plasma derived from platelet buffy coats during storage at room temperature. An application of ProteoMiner™ technology.

The present study was aimed at revealing new insights into the analysis of storage-related processes occurring in the supernatants of platelet concentrates (PCs) derived from pooled buffy coats suspended in whole plasma. To reduce the dynamic range of plasma protein concentrations and access low-abundance proteins, we made use of a solid-phase combinatorial peptide ligand library, known under the trade name of ProteoMiner™. Afterwards, two-dimensional electrophoresis (2-DE) was coupled with mass spectrometry (MS) to reveal changes in proteomic profiles. Several storage-induced protein alterations were identified including changes to major plasma proteins. In particular, a precursor of the secretory form of clusterin was shown to accumulate during storage of PC supernatants, together with platelet-derived tropomyosin, suggesting a progressive loss of platelet integrity. Platelet-released proteins following activation have also been detected (alpha-1-B-glycoprotein, kininogen-1, and serpin proteinase inhibitor 8). Moreover, specific protein fragments (vitronectin, plakoglobin, hornerin, and apolipoprotein A-IV) were found to be modulated upon storage, possibly indicating a time-dependent buffy-coat PC deterioration. Globally, our findings provided the disclosure of unique proteins in PC supernatants with respect to previous studies conducted in similar experimental conditions, suggesting ProteoMiner enrichment technology to be a possible complementary tool in the identification of diagnostically relevant proteins as age/quality biomarkers of therapeutic products.

Plasma gelsolin protein: a candidate biomarker for hepatitis B-associated liver cirrhosis identified by proteomic approach.

BACKGROUND: Despite the significant improvement in internal medicine and supportive therapy in recent years, liver fibrosis/cirrhosis remains a serious health issue in hepatitis B virus (HBV) infected patients. Invasive liver biopsy is presently the best means of diagnosing cirrhosis, but it carries a significant risk and has well recognised limitations such as sampling error, hence the importance in developing early diagnosis biomarkers. With this aim, we performed a pilot proteomic study to assess this as a strategy for plasma marker detection in patients suffering from HBV-associated liver cirrhosis. METHODS: Plasma from eight chronic HBV-infection patients and from eight HBV-related cirrhotic patients were selected and proteome profiles were created by two-dimensional electrophoresis. The strategy included the use of ProteoMiner enrichment kit for the reduction of highly abundance proteins (e.g. albumin and IgG) prior to proteomic analyses with the goal to improve detection of novel candidate markers. RESULTS: One reproducible spot was found to be completely repressed in plasma samples from cirrhotic patients and mass spectrometry analysis identified this a specific variant of the gelsolin actin-depolymerizing factor. Though further investigations are needed, especially in term of clinical validation, to our knowledge this is the first time that gelsolin is proposed as potential biomarker in HBV-related liver pathologies. CONCLUSIONS: Our findings confirm the potential utility of gelsolin either as a prognostic marker or a replacement therapeutic agent to alleviate liver injury.