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Listeria monocytogenes presents a dimorphism associated to the SecA2 activity with cells having a normal rod shape or a dysmorphic elongated filamentous form. Besides variation of the cell and colony morphotype, this cell differentiation has profound ecophysiological and physiopathological implications with collateral effects on virulence and pathogenicity, biotope colonisation, bacterial adhesion and biofilm formation. This suggests the SecA2-only protein export could influence the listerial cell surface, which was investigated first by characterising its properties in L. monocytogenes wt and secA2. The degree of hydrophilicity and Lewis acid-base properties appeared significantly affected upon SecA2 inactivation. As modification of electrostatic properties would owe to modification in the composition of cell-surface proteins, the proteosurfaceome was further investigated by shotgun label-free proteomic analysis with a comparative relative quantitative approach. Following secretomic analysis, the protein secretion routes of the identified proteins were mapped considering the cognate transport and post-translocational maturation systems, as well as protein categories and subcellular localisation. Differential protein abundance profiles coupled to network analysis revealed the SecA2 dependence of 48 proteins, including some related to cell envelope biogenesis, translation and protein export, which could account for modifications of adhesion and cell properties of L. monocytogenes upon SecA2 inactivation. This investigation unravelled the profound influence of SecA2 activity on the cell surface properties and proteosurfaceome of L. monocytogenes, which provides advanced insights about its ecophysiopathology. Significance L. monocytogenes is a foodborne zoonotic pathogen and etiological agent of human listeriosis. This species presents a cellular dimorphism associated to the SecA2 activity that has profound physiopathological and ecophysiological implications with collateral effects on bacterial virulence and colonisation. To explore the influence of the SecA2-only protein export on the listerial cell, the surface properties of L. monocytogenes expressing or depleted of SecA2 was characterised by microelectrophoresis, microbial affinity to solvents and contact angles analyses. As modifications of hydrophilicity and Lewis acid-base electrostatic properties would owe to modification in the composition of cell-surface proteins, the proteinaceous subset of the surfaceome, i.e. the proteosurfaceome, was investigated further by shotgun label-free proteomic analysis. This subproteome appeared quite impacted upon SecA2 inactivation with the identification of proteins accounting for modifications in the cell surface properties. The profound influence of SecA2 activity on the cell surface of L. monocytogenes was unravelled, which provides advanced insights about its ecophysiopathology., INRAE (“Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement”, previously called INRA, “Institut National de la Recherche Agronomique”), NCN (“Narodowe Centrum Nauki”) National Science Centre Poland (n°2013/09/B/NZ6/00710), ANR (“Agence National de la Recherche”) PathoFood project (n°ANR-17-CE21-0002), COST (European Cooperation in Science and Technology) Action FA1202 BacFoodNet, RMT (“Réseau Mixte Technologique”) CHLEAN (“Conception Hygiénique des Lignes et Equipements et Amélioration de la Nettoyabilité pour une alimentation saine et sure”) and France-Poland CampusFrance EGIDE PHC (“Programme Hubert Curien”) POLONIUM 2013 (n°28298ZE), info:eu-repo/semantics/publishedVersion

Introduction. The peripheral layers (PL) of wheat, including the aleurone layer (AL), are an important source of micronutrients. AL is excluded, and mainly used for animal feed, although these tissues have significant nutritional potential as they contain most micronutrients, phytochemicals and fiber, and could improve the nutritional quality of foods. Objective. A proteomic approach was used to reveal major protein differences in the aleurone layer (AL) of mature grain between four wheat species: T. Aestivum, and T. spelta (6X), T. durum (4X), and T. monococum (2X). Materiel and methods. In each species, one representative cultivar was used for total AL protein extraction. Two-dimensional electrophoresis of AL proteins revealed 1380, 1355, 1120, and 973 Coomassie stained spots, respectively. Results. A total of 334 spots showed quantitative or qualitative (presence/absence) differences between the four cultivars. T. Aestivum, and T. spelta had 90.9% and 92.6% of their AL proteome, identical, respectively. Only 25 spots were significantly different between the two hexaploid cultivars. AL proteins, encoded by A genome, were mainly expressed in polyploid species. Percentages of proteins, encoded by A genome, was 85%, in tetraploid species, and 70% in the hexaploid spelt. Eighty spots proteins, that are different qualitatively and quantitatively, were identified by mass spectrometry, and data mining, and were classified in 5 biological processes, and 12 functional categories. Conclusion. The major differences between species are, particularly, due to storage globulins (22, 11, and 1 of Glo-3, Glo-3B, Glo-3C, respectively), stress related proteins, including antioxidant proteins, like 1-Cys peroxiredoxin, and manganese superoxide dismutase, defence proteins like xylanase, serpin3, and heat shock proteins.

International audience; Among diarrheagenic E. coli (DEC), enterohaemorrhagic E. coli (EHEC) are the most virulent anthropozoonotic agents. The ability of bacterial cells to functionally interact with their surrounding essentially relies on the secretion of different protein effectors. To experimentally determine the repertoire of extracytoproteins in E. coli O157:H7, a subproteomic analysis was performed not only considering the extracellular milieu but the cell surface and outer membrane vesicles. Following a secretome-based approach, the proteins trafficking from the interior to the exterior of the cell were depicted considering cognate protein transport systems and subcellular localisation. Label-free quantitative analysis of the proteosurfaceome, proteovesiculome and exoproteome from E. coli O157:H7 grown in three different nutrient media revealed differential protein expression profiles and allowed defining the core and variant subproteomes. Network analysis further revealed the higher abundance of some protein clusters in chemically defined medium over rich complex medium, especially related to some outer membrane proteins, ABC transport and Type III secretion systems. This first comprehensive study of the EHEC secretome unravels the profound influence of environmental conditions on the extracytoplasmic proteome, provides new insight in the physiology of E. coli O157:H7 and identifies potentially important molecular targets for the development of preventive strategies against EHEC/STEC. Significance: Escherichia coli O157:H7 is responsible for severe diarrhoea especially in young children. Despite years of investigations, the global view of the extracytoplasmic proteins expressed in this microorganism was eluded. To provide the first comprehensive view of the secretome landscape of E. coli O157:H7, the exoproteome, proteosurfaceome and proteovesiculome were profiled using growth conditions most likely to induce changes in bacterial protein secretion. The profound influence of growth conditions on the extracytoplasmic proteome was unravelled and allowed identifying the core and variant subproteomes. Besides new insight in the physiology of enterohaemorrhagic E. coli, these proteins potentially constitute important molecular targets for the development of preventive strategies.

International audience; Food-derived bioactive peptides have generated an increasing interest in the field of health and well-being research. They can act either against the metabolic syndrome, participate in regulating the oxidation balance or act on the immune system. The aim of this study is to develop a workflow to generate bioactive peptides from three porcine offals namely, heart, liver, and lung and one muscle the Longissimus Dorsi, by combining in silico and in vitro approaches. Bioinformatics tools (e.i. BIOPEP and Uniprot) permitted to orientate the choice of enzymes for generating abundant bioactive peptides from the four studied porcine products. With papain and subtilisin, the main bioactivities potentially released were ACE inhibitors, DPP4 inhibitors and antioxidant peptides. An in vitro validation study using papain and subtilisin demonstrated high DPP4 inhibitors and antioxidant bioactivities for the generation of peptides. This work allowed: i) the identification of all proteins that composed porcine heart, liver, lung and LD muscle that could be useful for the scientific community, ii) the development of a workflow to select most abundant proteins in a product while considering abundance factors and iii) the potential of porcine meat and offals to generate DPP4 inhibitors and antioxidant peptides. However, there is still a need in developing new tools in order to face limitations of mass spectrometry for the identification of peptides with less than six amino acids. Such a work may contribute to the development of the circular economy and the innovative creation of value-added products from animal production.

International audience; We studied the kinetics of peptide release during the gastric digestion of meat proteins in vivo, in view to predicting the release of bioactive peptides further on in the digestive tract. Six mini pigs fitted with gastric cannulas received a meal with cooked beef as protein source. Digesta was collected at regular time intervals up to 5½ h. The peptides generated by the gastric digestion of meat were identified and quantified using label-free LC MS, thereafter subjected to in silico digestion mimicking the action of intestinal enzymes. Three clusters of proteins presenting similar evolutions according to their dynamic hydrolysis were obtained. This study clearly improves the in silico prediction of the intestinal release of bioactive peptides by mapping meat protein degradation in the stomach in an in vivo model. Knowledge of the conformation of the peptides released in the stomach further improves this prediction.

Matrix assisted laser desorption/ionization (MALDI) mass spectrometry imaging is a powerful tool that opens new research opportunities in the field of biology. In this work, predictive model was developed to discriminate metabolic myofiber types using the MALDI spectral data. Rat skeletal muscles are constituted of type I and type IIA fiber, which have an oxidative metabolism for glycogen degradation, and type IIX and type IIB fiber which have a glycolytic metabolism, present in different proportions according to the muscle function and physiological state. So far, myofiber type is determined by histological methods that are time consuming. Thanks to the predictive model, we were able to predict not only the metabolic fiber type but also their location, on the same muscle section that was used for MALDI imaging. Copyright © 2017 John Wiley & Sons, Ltd.

Natural collagen is easily available from animal tissues such as bones. Main limitations reported in the use of natural collagen are heterogeneity and loss of integrity during recovery. However, its natural complexity, functionality and bioactivity still remain to be achieved through synthetic and recombinant ways. Variability of physicochemical properties of collagen extracted from bovine bone by acetic acid was then investigated taking into account endogenous and exogenous factors. Endogenous: bovine’s bones age (4 and 7 years) and anatomy (femur and tibia); exogenous: thermal treatments (spray-drying and lyophilisation). Scanning electron microscopy, spectroscopy (EDS, FTIR, UV/Vis and CD), differential scanning calorimetry (DSC), centesimal composition, mass spectrometry, amino acids and zeta-potential analysis were used for the purpose. Age correlated negatively with yield of recovery and positively with minerals and proteoglycans content. Comparing the anatomy, higher yields were found for tibias, and higher stability of tibias collagen in solution was noticed. Whatever the age and the anatomy, collagens were able to renature and to self-assemble into tri-dimensional structures. Nonetheless thermal stability and kinetics of renaturation were different. Variability of natural collagen with bone age and anatomy, and drying methodology, may be a crucial advantage to conceive tailor-made applications in either the biological or technical sector.

Obesity induced by overfeeding ultimately can lead to nonalcoholic fatty liver disease, whereas dietary fiber consumption is known to have a beneficial effect. We aimed to determine if a supplementation of a mix of fibers (inulin, resistant starch and pectin) could limit or alleviate overfeeding-induced metabolic perturbations. Twenty female minipigs were fed with a control diet (C) or an enriched fat/sucrose diet supplemented (O + F) or not (O) with fibers. Between 0 and 56 days of overfeeding, insulin (+88%), HOMA (+102%), cholesterol (+45%) and lactate (+63%) were increased, without any beneficial effect of fibers supplementation. However, fibers supplementation limited body weight gain (vs. O, −15% at D56) and the accumulation of hepatic lipids droplets induced by overfeeding. This could be explained by a decreased lipids transport potential (−50% FABP1 mRNA, O + F vs. O) inducing a down-regulation of regulatory elements of lipids metabolism / lipogenesis (−36% SREBP1c mRNA, O + F vs. O) but not to an increased oxidation (O + F not different from O and C for proteins and mRNA measured). Glucose metabolism was also differentially regulated by fibers supplementation, with an increased net hepatic release of glucose in the fasted state (diet × time effect, P

International audience; Adipose tissue (AT) deposits, either intramuscular (i.e., marbling) or at the carcass level, are major economic drivers in the beef industry. To identify biomarkers and unravel mechanisms of AT deposition, we combined gelbased and gel-free methods and we mined the differential proteome of the longissimus thoracis from cows differing by two levels of both carcass and muscular adiposities (CMA). We identified 47 proteins with abundances that varied according to CMA. We listed 26 new candidate biomarkers of marbling and confirmed 21 proteins already proposed in the literature. Seven proteins involved in glycolysis or gluconeogenesis were the least abundant, while 14 proteins related to oxidative metabolism, slow-type muscle or retinoic acid metabolism were the most abundant in the high adiposity group. We highlighted eight proteins as differentially abundant and correlated with both CMA, thereby providing the first list of putative biomarkers of carcass adiposity. These proteins would be targeted in future studies aiming to categorize adiposity in cattle.

International audience; In humans, meat ensures the supply of proteins with high nutritional value and indispensable amino acids. The main goal of the present study was to compare the degradation of meat proteins in adult and elderly digestive conditions. Cooked meat was subjected to in vitro digestion in the dynamic multi-compartmental TIM (TNO gastroIntestinal Model) system. Digestibility and bioaccessibility were determined using nitrogen balance and digestion products were identified using mass spectrometry. The TIM model was adapted according to in vivo data to mimic the specific digestive conditions of elderly people. Meat protein digestibility and bioaccessibility were around 96 and 60% respectively and were not influenced by age (P > 0.05). As much as 800 peptides were identified in the duodenal and jejunal compartments issued from 50 meat proteins with a percentage of coverage varying from 13 to 69%. Six proteins, mainly from the cytosol, were differentially hydrolyzed under the adult and elderly digestive conditions. Pyruvate kinase was the only protein clearly showing a delay in its degradation under elderly digestive conditions. This study provides significant insights into the understanding of meat protein dynamic digestion. Such data will be helpful to design in vivo studies aiming to evaluate dietary strategies that can attenuate muscle mass loss and more generally maintain a better quality of life in the elderly population.

Epub 2018 Jul 30; MALDI-TOF Mass spectrometry Imaging (MSI) is a surface-sampling technology that can determine spatial information and relative abundance of analytes directly from biological samples. Human listeriosis cases are due to the ingestion of contaminated foods with the pathogenic bacteria Listeria monocytogenes. The reduction of water availability in food workshops by decreasing the air relative humidity (RH) is one strategy to improve the control of bacterial contamination. This study aims to develop and implement an MSI approach on L. monocytogenes biofilms and proof of concept using a dehumidified stress condition. MSI allowed examining the distribution of low molecular weight proteins within the biofilms subjected to a dehumidification environment, mimicking the one present in a food workshop (10 °C, 75% RH). Furthermore, a LC-MS/MS approach was made to link the dots between MSI and protein identification. Five identified proteins were assigned to registered MSI m/z, including two cold-shock proteins and a ligase involved in cell wall biogenesis. These data demonstrate how imaging can be used to dissect the proteome of an intact bacterial biofilm giving new insights into protein expression relating to a dehumidification stress adaptation. Data are available via ProteomeXchange with identifier PXD010444.BIOLOGICAL SIGNIFICANCE:The ready-to-eat food processing industry has the daily challenge of controlling the contamination of surfaces and machines with spoilage and pathogenic microorganisms. In some cases, it is a lost cause due to these microorganisms' capacity to withstand the cleaning treatments, like desiccation procedures. Such a case is the ubiquitous Gram-positive Bacterium Listeria monocytogenes. Its surface proteins have particular importance for the interaction with its environment, being important factors contributing to adaptation to stress conditions. There are few reproducibly techniques to obtain the surface proteins of Gram-positive cells. Here, we developed a workflow that enables the use of MALDI imaging on Gram-positive bacterium biofilms to study the impact of dehumidification on sessile cells. It will be of the most interest to test this workflow with different environmental conditions and potentially apply it to other biofilm-forming bacteria.

International audience; Surface proteins are the major factor for the interaction between bacteria and its environment, playing an important role in infection, colonisation, virulence and adaptation. However, the study of surface proteins has proven difficult mainly due to their hydrophobicity and/or relatively low abundance compared with cytoplasmic proteins. To overcome these issues new proteomic strategies have been developed, such as cell-surface protein labelling using biotinylation reagents. Sulfo-NHS-SS-biotin is the most commonly used reagent to investigate the proteins expressed at the cell surface of various organisms but its use in lipopolysaccharidic diderm bacteria (archetypical Gram-negative bacteria) remains limited to a handful of species. While generally pass over in silence, some periplasmic proteins, but also some inner membrane lipoproteins, integral membrane proteins and cytoplasmic proteins (cytoproteins) are systematically identified following this approach. To limit cell lysis and diffusion of the sulfo-NHS-SS-biotin through the outer membrane, biotin labelling was tested over short incubation times and proved to be as efficient for 1 min at room temperature. To further limit labelling of protein located below the outer membrane, the use of high-molecular weight sulfo-NHS-PEG4-bismannose-SS-biotin appeared to recover differentially cell-envelope proteins compared to low-molecular weight sulfo-NHS-SS-biotin. Actually, the sulfo-NHS-SS-biotin recovers at a higher extent the proteins completely or partly exposed in the periplasm than sulfo-NHS-PEG4-bismannose-SS-biotin, namely periplasmic and integral membrane proteins as well as inner membrane and outer membrane lipoproteins. These results highlight that protein labelling using biotinylation reagents of different sizes provides a sophisticated and accurate way to differentially explore the cell envelope proteome of lipopolysaccharidic diderm bacteria. SIGNIFICANCE: While generally pass over in silence, some periplasmic proteins, inner membrane lipoproteins (IMLs), integral membrane proteins (IMPs) and cytoplasmic proteins (cytoproteins) are systematically identified following cell-surface biotin labelling in lipopolysaccharidic diderm bacteria (archetypal Gram-negative bacteria). The use of biotinylation molecules of different sizes, namely sulfo-NHS-SS-biotin and sulfo-NHS-PEG4-bismannose-SS-biotin, was demonstrated to provide a sophisticated and accurate way to differentially explore the cell envelope proteome of lipopolysaccharidic diderm bacteria.

Background: Fluoroquinolone resistance in nontyphoidal Salmonella is a situation of serious and international concern, particularly in S. Typhimurium DT104B multiresistant strains. Although known to be multifactorial, fluoroquinolone resistance is still far from a complete understanding. Methods: Subproteome changes between an experimentally selected fluoroquinolone-resistant strain (Se6-M) and its parent strain (Se6), and also in Se6-M under ciprofloxacin (CIP) stress, were evaluated in order to give new insights into the mechanisms involved. Proteomes were compared at the intracellular and membrane levels by a 2-DE~LC-MS/MS and a shotgun LC-MS/MS approach, respectively. Results: In total, 35 differentially abundant proteins were identified when comparing Se6 with Se6-M (25 more abundant in Se6 and 10 more abundant in Se6-M) and 82 were identified between Se6-M and Se6-M+CIP (51 more abundant in Se6-M and 31 more abundant under ciprofloxacin stress). Conclusion: Several proteins with known and possible roles in quinolone resistance were identified which provide important information about mechanism-related differential protein expression, supporting the current knowledge and also leading to new testable hypotheses on the mechanism of action of fluoroquinolone drugs. info:eu-repo/semantics/publishedVersion

Epub ahead of print; Gluten-forming storage proteins play a major role in the viscoelastic properties of wheat dough through the formation of a continuous proteinaceous network. The high-molecular-weight glutenin subunits represent a functionally important subgroup of gluten proteins by promoting the formation of large glutenin polymers through interchain disulphide bonds between glutenin subunits. Here, we present evidences that y-type glutenin subunits encoded at the Glu-B1 locus are prone to proteolytic processing at the C-terminus tail, leading to the loss of the unique cysteine residue present at the C-terminal domain. Results obtained by intact mass measurement and immunochemistry for each proteoform indicate that the proteolytic cleavage appears to occur at the carboxyl-side of two conserved asparagine residues at the C-terminal domain start. Hence, we hypothesize that the responsible enzymes are a class of cysteine endopeptidases - asparaginyl endopeptidases - described in post-translational processing of other storage proteins in wheat. Biological significance The reported study provides new insights into wheat storage protein maturation. In view of the importance of gluten proteins on dough viscoelastic properties and end-product quality, the reported C-terminal domain cleavage of high-molecular-weight glutenin subunits is of particular interest, since this domain possesses a unique conserved cysteine residue which is assumed to participate in gluten polymerization.

International audience; The aleurone layer (AL) is an inner tissue of the wheat grain. It contains micronutrients, vitamins, antioxidants and fibre, and can greatly increase the nutritional quality of flour if it is not removed from the kernel with the bran. The AL of mature kernels of three varieties of the two major cultivated wheat species T. aestivum (genome A, B and D) and T. monococcum (genome A) were manually dissected and analyzed using two-dimensional gel-based proteomics. In T. monococcum although composed of only genome A, the maximum number of Coomassie stained AL spots was close to the number found in the bread wheat varieties (1320 and 1258, respectively). Inter-variety variation in spots was higher in the three T. monococcum varieties (103 spots) than in the three T. aestivum varieties (79 spots). Comparison of the two species revealed that only 88 spots differed significantly either in abundance or presence/absence. The B and D genome did not drastically modify the AL proteome, as demonstrated by the fact that 93% of the spots present in T. Monococcum AL spots were also present in T. aestivum. Proteins which differed within and between species were identified using MALDI-TOF and LC-MS/MS Mass Spectrometry. Among the 182 spots that differed, 115 were identified, 53 differed between the two species and 44 (83%) were globulin (Glo) storage proteins. The remarkable environmental stability of the AL proteome previously observed in T. durum and T. aestivum species was confirmed in the variety T. monococcum DV92, grown for two consecutive years in field conditions. Only 15 proteins (out of 1320 AL spots) exhibited significant quantitative variations.

International audience; Mass spectrometry imaging (MSI) is a powerful tool to visualize the spatial distribution of molecules on a tissue section. The main limitation of MALDI-MSI of proteins is the lack of direct identification. Therefore, this study focuses on a MSI~LC-MS/MS-LF workflow to link the results from MALDI-MSI with potential peak identification and label-free quantitation, using only one tissue section. At first, we studied the impact of matrix deposition and laser ablation on protein extraction from the tissue section. Then, we did a back-correlation of the m/z of the proteins detected by MALDI-MSI to those identified by label-free quantitation. This allowed us to compare the label-free quantitation of proteins obtained in LC-MS/MS with the peak intensities observed in MALDI-MSI. We managed to link identification to nine peaks observed by MALDI-MSI. The results showed that the MSI~LC-MS/MS-LF workflow (i) allowed us to study a representative muscle proteome compared to a classical bottom-up workflow; and (ii) was sparsely impacted by matrix deposition and laser ablation. This workflow, performed as a proof-of-concept, suggests that a single tissue section can be used to perform MALDI-MSI and protein extraction, identification, and relative quantitation.

Saccharomyces cerevisiae plays a primordial role in alcoholic fermentation and has a vast worldwide application in the production of fuel-ethanol, food and beverages. The dominance of S. cerevisiae over other microbial species during alcoholic fermentations has been traditionally ascribed to its higher ethanol tolerance. However, recent studies suggested that other phenomena, such as microbial interactions mediated by killer-like toxins, might play an important role. Here we show that S. cerevisiae secretes antimicrobial peptides (AMPs) during alcoholic fermentation that are active against a wide variety of wine-related yeasts (e.g. Dekkera bruxellensis) and bacteria (e.g. Oenococcus oeni). Mass spectrometry analyses revealed that these AMPs correspond to fragments of the S. cerevisiae glyceraldehyde 3-phosphate dehydrogenase (GAPDH) protein. The involvement of GAPDH-derived peptides in wine microbial interactions was further sustained by results obtained in mixed cultures performed with S. cerevisiae single mutants deleted in each of the GAPDH codifying genes (TDH1-3) and also with a S. cerevisiae mutant deleted in the YCA1 gene, which codifies the apoptosis-involved enzyme metacaspase. These findings are discussed in the context of wine microbial interactions, biopreservation potential and the role of GAPDH in the defence system of S. cerevisiae. info:eu-repo/semantics/publishedVersion

The finding of new diagnostic and prognostic markers of local radiation injury, and particularly of the cutaneous radiation syndrome, is crucial for its medical management, in the case of both accidental exposure and radiotherapy side effects. Especially, a fast high-throughput method is still needed for triage of people accidentally exposed to ionizing radiation. In this study, we investigated the impact of localized irradiation of the skin on the early alteration of the serum proteome of mice in an effort to discover markers associated with the exposure and severity of impending damage. Using two different large-scale quantitative proteomic approaches, 2D-DIGE-MS and SELDI-TOF-MS, we performed global analyses of serum proteins collected in the clinical latency phase (days 3 and 7) from non-irradiated and locally irradiated mice exposed to high doses of 20, 40 and 80 Gy which will develop respectively erythema, moist desquamation and necrosis. Unsupervised and supervised multivariate statistical analyses (principal component analysis, partial-least square discriminant analysis and Random Forest analysis) using 2D-DIGE quantitative protein data allowed us to discriminate early between non-irradiated and irradiated animals, and between uninjured/slightly injured animals and animals that will develop severe lesions. On the other hand, despite a high number of animal replicates, PLS-DA and Random Forest analyses of SELDI-TOF-MS data failed to reveal sets of MS peaks able to discriminate between the different groups of animals. Our results show that, unlike SELDI-TOF-MS, the 2D-DIGE approach remains a powerful and promising method for the discovery of sets of proteins that could be used for the development of clinical tests for triage and the prognosis of the severity of radiation-induced skin lesions. We propose a list of 15 proteins which constitutes a set of candidate proteins for triage and prognosis of skin lesion outcomes.

International audience; Hsp27—encoded by HspB1—is a member of the small heat shock proteins (sHsp, 12–43 kDa (kilodalton)) family. This protein is constitutively present in a wide variety of tissues and in many cell lines. The abundance of Hsp27 is highest in skeletal muscle, indicating a crucial role for muscle physiology. The protein identified as a beef tenderness biomarker was found at a crucial hub in a functional network involved in beef tenderness. The aim of this study was to analyze the proteins impacted by the targeted invalidation of HspB1 in the Tibialis anterior muscle of the mouse. Comparative proteomics using two-dimensional gel electrophoresis revealed 22 spots that were differentially abundant between HspB1-null mice and their controls that could be identified by mass spectrometry. Eighteen spots were more abundant in the muscle of the mutant mice, and four were less abundant. The proteins impacted by the absence of Hsp27 belonged mainly to calcium homeostasis (Srl and Calsq1), contraction (TnnT3), energy metabolism (Tpi1, Mdh1, PdhB, Ckm, Pygm, ApoA1) and the Hsp proteins family (HspA9). These data suggest a crucial role for these proteins in meat tenderization. The information gained by this study could also be helpful to predict the side effects of Hsp27 depletion in muscle development and pathologies linked to small Hsps.

International audience; UNLABELLED: Antimicrobial resistance is a growing public health threat worldwide that is still far from a complete understanding. Salmonella Typhimurium DT104 multiresistant strains with additional quinolone resistance are highly adaptive and have been responsible for global outbreaks and high mortality. In order to give new insights about the resistance mechanisms involved, the developed work aimed to point out subproteome changes between a DT104B clinical strain (Se20) that acquired quinolone resistance after patient treatment and an in vitro induced clonally related highly-resistant mutant (Se6-M). The intracellular subproteomes were compared by a 2-DE/LC-MS/MS approach and a total of 50 unique proteins were identified (32 more abundant in Se20 and 18 more abundant in Se6-M). The membrane subproteomes were analysed by a shotgun LC-MS/MS approach, where 7 differentially abundant proteins were identified (5 more abundant in Se6-M and 2 more abundant in Se20). Several proteins known to be directly related to quinolone resistance mechanisms (AAC(6')-Ib-cr4, OmpC, OmpD, OmpX, etc.) and MipA, recently reported as novel antibiotic resistance-related protein, were identified. Other proteins (Fur, SodA, SucB, AtpD/AtpG, OmpC, GltI, CheM/CheB, etc.) reflecting the metabolic re-adjustments occurred in each strain in order to acquire quinolone resistance were also identified. Moreover, proteins involved in lipopolysaccharide biosynthesis (RfbF, RfbG, GmhA) and export (LptA) were detected, supporting the importance of exploring these proteins as targets for the development of new antimicrobial agents. In conclusion, this study provides new insights into the mechanisms involved in the acquisition of antibiotic resistance, which can be highly valuable for the development of improved therapeutic strategies. BIOLOGICAL SIGNIFICANCE: This comparative proteomic study revealed a large number of differentially regulated proteins involved in antibiotic resistance which can be of great value to drug discovery, research and development programmes.

International audience; We aimed to identify and quantify the peptides generated during in vitro digestion of cooked meat by liquid chromatography coupled with high resolution mass spectrometer. A total of 940 non-redundant peptides in the gastric compartment and 989 non-redundant peptides in the intestinal compartment were quantified and identified. Among the 71 different proteins identified, 43 meat proteins were found in the two digestive compartments, 20 proteins were specific to the gastric compartment and 8 proteins to the intestinal compartment. In terms of estimation, the proteins involved in muscle contraction and structure were preferentially enzymatically hydrolyzed in the small intestine. The effect of cooking provided different but less clear patterns of digestion. To the best of our knowledge, this constitutes the highest number of peptides identified in beef meat digests and provides a comprehensive database for meat protein digestion associated with cooking conditions. Such quantitative and qualitative differences may have important nutritional consequences.

Background Plant cell wall (PCW) polysaccharides and especially xylans constitute an important part of human diet. Xylans are not degraded by human digestive enzymes in the upper digestive tract and therefore reach the colon where they are subjected to extensive degradation by some members of the symbiotic microbiota. Xylanolytic bacteria are the first degraders of these complex polysaccharides and they release breakdown products that can have beneficial effects on human health. In order to understand better how these bacteria metabolize xylans in the colon, this study was undertaken to investigate xylan breakdown by the prominent human gut symbiont Bacteroides xylanisolvens XB1AT. Results Transcriptomic analyses of B. xylanisolvens XB1AT grown on insoluble oat-spelt xylan (OSX) at mid- and late-log phases highlighted genes in a polysaccharide utilization locus (PUL), hereafter called PUL 43, and genes in a fragmentary remnant of another PUL, hereafter referred to as rPUL 70, which were highly overexpressed on OSX relative to glucose. Proteomic analyses supported the up-regulation of several genes belonging to PUL 43 and showed the important over-production of a CBM4-containing GH10 endo-xylanase. We also show that PUL 43 is organized in two operons and that the knockout of the PUL 43 sensor/regulator HTCS gene blocked the growth of the mutant on insoluble OSX and soluble wheat arabinoxylan (WAX). The mutation not only repressed gene expression in the PUL 43 operons but also repressed gene expression in rPUL 70. Conclusion This study shows that xylan degradation by B. xylanisolvens XB1AT is orchestrated by one PUL and one PUL remnant that are linked at the transcriptional level. Coupled to studies on other xylanolytic Bacteroides species, our data emphasize the importance of one peculiar CBM4-containing GH10 endo-xylanase in xylan breakdown and that this modular enzyme may be used as a functional marker of xylan degradation in the human gut. Our results also suggest that B. xylanisolvens XB1AT has specialized in the degradation of xylans of low complexity. This functional feature may provide a niche to all xylanolytic bacteria harboring similar PULs. Further functional and ecological studies on fibrolytic Bacteroides species are needed to better understand their role in dietary fiber degradation and their impact on intestinal health. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2680-8) contains supplementary material, which is available to authorized users.

et al., Escherichia coli is a commensal microorganism of the gastrointestinal tract of animals and humans and it is an excellent model organism for the study of antibiotic resistance mechanisms. The resistance transmission and other characteristics of bacteria are based on different types of gene transfer occurring throughout the bacterial evolution. One of which is horizontal gene transfer that allows us to understand the ability of bacteria to acquire new genes. One dimensional and two dimensional electrophoresis (2-DE) techniques were performed in order to identify and characterize the proteome of two E. coli strains: Electromax DH10B, a transformation-ready strain; and TF-Se20, the Electromax DH10B that contains the aac(6′)-Ib-cr4-harboring pMdT1 plasmid. After 2-DE and subsequent analysis by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), it was possible to identify 76 distinct proteins on the TF-Se20 strain, whereas 71 had a known function. From Electromax DH10B strain, 72 different proteins were identified of which 71 were associated with a biological process. The protein of interest, aminoglycoside N-(6′)-acetyltransferase type 1, was identified by MALDI-TOF MS. The liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique was performed to determine its sequence. Seventy six percent of the acetylase sequence was reconstructed only in the TF-Se20 strain, representing the single protein associated to antibiotic resistance. MALDI-TOF MS and LC-MS/MS approaches allowed us to determine the total proteome of both strains, as well as the acetylase sequence. Both of them enhance the ability to obtain more accurate information about the mechanisms of antimicrobial resistance. The pMdT1 plasmid brings a new perspective in understanding the metabolic processes that lead to antibiotic resistance. Biological significance This study highlights the importance of proteomics and bioinformatics in understanding mechanisms of gene transfer and antibiotic resistance. These two approaches allow to compare the protein expression in different samples, as well as different biological processes related to each protein., The authors are grateful to the Research Unit on Applied Molecular Biosciences (UCIBIO) which is financed by national funds from FCT/MEC (UID/Multi/04378/2013) and co-financed by the ERDF under the PT2020 Partnership Agreement (POCI-01-0145-FEDER-007728).

International audience; The aleurone layer (AL) is one of inner tissues removed from the grain with the wheat bran. It is the main source of vitamins, minerals and antioxidants of potential nutritional value in the wheat kernel. The AL of three varieties of each of the two main species of wheat, Triticum aestivum (ABD) and Triticum durum (AB), were manually dissected and analysed using two-dimensional gel-based proteomics. A total of 1258 and 1109 Coomassie-stained spots were detected in the AL of representatives of the ABD and AB genomes. In two varieties (T aestivum Chinese Spring and T durum Bidi17), grown in two different years with full fungicide protection, no quantitative or qualitative (presence/absence) differences in spots were detected, suggesting that AL proteome is strongly genetically controlled. Comparison within and between species revealed a total of 339 AL significant protein spots. Among these spots, 30.8% differed within T. aestivum and 56.5% within T durum varieties, whereas only 12.7% differed between the two species. Among the 142 AL proteins identified using MALDI-TOF and LC-MS/MS, 57% were globulin type storage proteins (Glo-3, Glo-3B, Glo-3C, Glo-2), 16.2% were involved in carbohydrate metabolism and 17.6% in defence/stress pathways. These variations in AL proteome are discussed.

Proteomic analysis of albumins and globulins (alg) present in starchy endosperm of wheat (Triticum aestivum cv Récital), at 21 stages of grain development, led to the identification of 487 proteins. Four main developmental phases of these metabolic proteins, with three subphases in phase three and two in phase four, were shown. Hierarchical cluster analysis revealed nine major expression profiles throughout grain development. Classification of identified proteins in 17 different biochemical functions provided a uniform picture of temporal coordination among cellular processes. Proteins involved in cell division, transcription/translation, ATP interconversion, protein synthesis, protein transport, along with amino acid, lipid, carbohydrate and nucleotide metabolisms were highly expressed in early and early mid stages of development. Protein folding, cytoskeleton, and storage proteins peaked during the middle of grain development, while in later stages stress/defense, folic acid metabolism, and protein turn over were the abundant functional categories. Detailed analysis of stress/defense enzymes revealed three different evolutionary profiles. A global map with their predicted subcellular localizations and placement in grain developmental scale was constructed. The present study of complete grain development enriched our knowledge on proteome expression of alg, successively from endosperm cell division and differentiation to programmed cell death.

International audience; The aim of this study was to apply a proteomic approach for the characterisation of local chicken breeds. The experiment involved a total of 29 males of three local Italian chicken breeds: Pepoi, Padovana and Ermellinata di Rovigo. Sarcoplasmic protein fractions of breast muscle were analysed by 2-DE. Image analysis followed by statistical analysis enabled to differentiate groups of individuals based on the similarities of protein expression. Individuals were distinguished into clusters and groups, corresponding to the breed of origin. Distances among individuals, calculated using data on spot volumes, were used to draw a neighbour-joining tree, showing clear individual and breed grouping. The most relevant spots regarding breed differentiation were detected; 11 were identified by MS revealing preliminary evidences on the mechanisms of the breed differentiation process. The results evidenced the ability of proteomic analyses for the characterisation of chicken breeds.

International audience; The aim of the study was to delineate and compare the proteomic maps of two muscles of dry-cured ham: the biceps femoris and the semimembranosus. For this purpose, we used two-dimensional electrophoresis on a subcellular muscle fraction: insoluble protein in low ionic strength buffer. After protein identification by MALDI–TOF mass spectrometry and bioinformatic analyses, we found differences in expression levels in the two muscles. Seventy-three proteins or fragments were differentially expressed: 43 were over-represented in semimembranosus and 30 in biceps femoris. Although the study was performed on the insoluble protein fraction in low strength ionic buffer, protein and fragment identifications by mass spectrometry showed that most of the proteins were involved in energy metabolism. The differences observed between the two muscles can be explained by the differences in salt and moisture content in the course of dry-cured ham processing.

In bread wheat ( Triticum aestivum L.), waxy genes are present at three loci ( Wx-A1 , Wx-B1 and Wx-D1 ) and are responsible for amylose synthesis in the grain. Near isogenic lines (NILs) of the agronomic cultivar Tremie with either one, two or three waxy null alleles were used to study the genome response to these null alleles through proteomic analysis of starch granule associated proteins of mature grain. Among the 352 spots that were revealed, 86 varied significantly between NILs. The main differences were observed for the granule bound starch synthase (GBSS), product of the waxy genes. A strong relation (R 2 = 0.94) between the amount of GBSS per gram of starch granule and the amylose quantity in the grain was revealed through quantification of the GBSS in each NIL. The analysis of GBSS quantity for each NIL invalidated the additive hypothesis for the expression of this enzyme in ( Wx-A1a Wx-D1a Wx-B1b ) ( Wx-D1a Wx-B1a Wx-A1b ) and the normal form of Tremie. In addition, four proteins identified as inactive GBSS were increased (+144.9%) in the triple null isogenic form compared to the normal form of Tremie. The quantitative variations of the proteins present in starch granules support the idea of regulatory mechanisms between genomes.

International audience; Contractile and metabolic properties of bovine muscles play an important role in meat sensorial quality, particularly tenderness. Earlier studies based on Myosin heavy chain isoforms analyses and measurements of glycolytic and oxidative enzyme activities have demonstrated that the third trimester of foetal life in bovine is characterized by contractile and metabolic differentiation. In order to complete this data and to obtain a precise view of this phase and its regulation, we performed a proteomic analysis of Semitendinosus muscle from Charolais foetuses analysed at three stages of the third trimester of gestation (180, 210 and 260 days). The results complete the knowledge of important changes in the profiles of proteins from metabolic and contractile pathways. They provide new insights about proteins such as Aldehyde dehydrogenase family, Enolase, Dihydrolipoyl dehydrogenase, Troponin T or Myosin light chains isoforms. These data have agronomical applications not only for the management of beef sensorial quality but also in medical context, as bovine myogenesis appears very similar to human one.

International audience; Myogenesis is a complex process of which the underlying mechanisms are conserved between species, including birds and mammals. Despite a good understanding of the stages of myogenesis, many of the mechanisms involved in the regulation of proliferation of the successive myoblast generations, the cellular transitions cell proliferation/alignment of myoblasts/fusion of myoblasts into myotubes/differentiation of myofibres and the control of total myofibre number still remain unknown. An in vivo proteomic analysis of the semitendinosus muscle from Charolais foetuses, at three specific stages of myogenesis (60, 110 and 180 days postconception), was conducted using 2-DE and MS. Expression profiles of more than 170 proteins were revealed and analysed using two way hierarchical clustering and statistical analysis. Our studies identify, for the first time, distinct proteins of varied biological functions and protein clusters with myogenic processes, such as the control of cell cycle activity and apoptosis, the establishment of cellular metabolism and muscle contractile properties and muscle cell reorganisation. These results are of fundamental interest to the field of myogenesis in general, and more specifically to the control of muscle development in meat producing animals.

The role of Lactobacillus strains with bioprotective and technological potential on raw beef during 15 days of storage under vacuum at 7 °C was investigated. The assayed strains were able to grow on the meat, Lactobacillus curvatus CRL705 and Lactobacillus sakei 23K showing the highest competitiveness. A net increase of amino acids was determined in inoculated samples when compared to the control, this being maximal for Lactobacillus plantarum CRL681. Although an important endogenous activity of meat sarcoplasmic proteins was observed, the disappearance of protein bands and the generation of a new one were detected as a consequence of Lactobacillus growth. A synergistic effect of Lactobacillus in combination with the muscle proteolytic enzyme complex can be suggested. From the studied strains, the bacteriocin producer L. curvatus CRL705 may be considered as a good candidate to contribute to meat ageing by means of small peptides and free amino acids generation while improving shelf life. Fil: Fadda, Silvina G.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina Fil: Chambon, Christophe. Institut National de la Recherche Agronomique; Francia Fil: Champomier Vergès, Marie Christine. Institut National de la Recherche Agronomique; Francia Fil: Talon, Régine. Institut National de la Recherche Agronomique; Francia Fil: Vignolo, Graciela Margarita. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina

Two-dimensional electrophoresis was used to compare Longissimus sarcoplasmic protein abundance between two groups (tough meat and tender meat), defined on the basis of extreme Warner-Bratzler shear force values measured on cooked pork. Fourteen protein spots differed in quantity (P0.05) between the two groups and were identified. Adypocyte fatty acid binding protein and acyl-CoA binding protein involved in lipid traffic and in the control of gene expression regulating cell proliferation and differentiation, and Enoyl-CoA hydratase, aldose reductase and triosephosphate isomerase indirectly related to lipid metabolism were overrepresented in the tender group. The tender group was further characterized by increased levels of proteins involved in protein folding and polymerization (initiation factor elf-3beta, chaperonin subunit 2, profilin II). The results suggest that the lower post-cooking shear force could at least in part be related to muscle adipogenetic and/or myogenetic status of which the possible underlying mechanisms are discussed.

For many years Staphylococcus aureus has been recognized as an important human pathogen. In this study, the surfacome and exoproteome of a clinical sample of MRSA was analyzed. The C2355 strain, previously typed as ST398 and spa-t011 and showing a phenotype of multiresistance to antibiotics, has several resistance genes. Using shotgun proteomics and bioinformatics tools, 236 proteins were identified in the surfaceome and 99 proteins in the exoproteome. Although many of these proteins are related to basic cell functions, some are related to virulence and pathogenicity like catalase and isdA, main actors in S. aureus infection, and others are related to antibiotic action or eventually resistance like penicillin binding protein, a cell-wall protein. Studying the proteomes of different subcellular compartments should improve our understanding of this pathogen, a microorganism with several mechanisms of resistance and pathogenicity, and provide valuable data for bioinformatics databases., Graphical abstract, Highlights • We examine the surface proteome and exoproteome of multiresistant strains. • We identify bacterial infection proteins in the extracellular proteome. • Confirmation that moonlighting proteins will extend the localization data.

The aleurone layer (AL) is the grain peripheral tissue; it is rich in micronutrients, vitamins, antioxidants, and essential amino acids. This highly nutritive part of the grain has been less studied partly because its isolation is so laborious. In the present study, the ALs of Triticum aestivum (variety Recital) were separated manually at 15 stages of grain development. A total of 327 proteins were identified using 2-DE LC-MS/MS. They were classified in six main groups and 26 sub-groups according to their biochemical function. Proteomic analysis revealed seven different profiles distributed among three main development stages: (i) early AL development, with proteins involved in intense metabolic activities in the growth and development of the cell wall compounds; (ii) the intermediate stage, characterized by oxidative stress and defense proteins (65%) linked with loss of water in peripheral layers during grain filling; and (iii) AL maturation, involving the production of amino acids and the control of reactive oxidative species to enable the accumulation and maturation of globulins within the AL. The present study provides the first insights into developing proteome in the AL. We describe the numerous AL enzymes involved in the accumulation of storage protein and in the protection of the endosperm over time. Biological significance The hand dissection of wheat aleurone layer (AL) was carried in this study for the first time on fifteen developmental stages from cell differentiation to grain maturity. Three major phases were revealed over AL development: cell division activities, globulins storage, and grain protection. Enzymes related to metabolites and vitamins were abundantly expressed during the two first phases. In parallel to the progressive globulins accumulation, the final phase was characterized by key enzyme synthesis involved in energy production, amino-acids and antioxidant synthesis plus others to face hypoxia and dehydration of grain tissues.

As commonly seen in monoderm bacteria, Listeria monocytogenes possesses multiple membrane-bound signal peptidases of Type I (SPases I) called SipX, SipY and SipZ. In order to decipher their respective contribution in an integrated and global view, the complement of the secretome corresponding to the exoproteome was resolved by two-dimensional gel electrophoresis (2-DE). This was performed for L. monocytogenes sipX − , sipY − , sipZ − single mutants, as well as for Δ sipXY and Δ sipYZ double mutants, and then compared to that of the wild type strain. Remarkably, the amounts of listeriolysin O (LLO), phosphatidylcholine phospholipase C (PlcB) and zinc metalloproteinase Mpl in the extracellular milieu were significantly decreased upon inactivation of SipZ. For the majority of the Sec-secreted exoproteins identified, protein secretion was not affected by the inactivation of one or two of the SPases I, supporting the concept that the three SPases I have overlapping specificities for the cleavage of the signal peptides. The current study reveals that the role of SipZ as the major SPase I of L. monocytogenes applies only to a small subset of the secreted exoproteins. Rather than absolute, the notion of major and minor SPases thus appears to be relative. In addition to new insight into bacterial physiology, this investigation of the contribution of the SPases I to the exoproteome of L. monocytogenes paves the way for further characterization of other complements of the secretome under various environmental conditions. Biological significance L. monocytogenes encodes three orthologous signal peptidases of Type I (SPases I). SipZ improves the secretion efficiency for a subset of extracellular virulence factors. Multiple SPases I are functionally redundant for the majority of the Sec-secreted exoproteins of L. monocytogenes . The concepts of major and minor SPases are not absolute but relative.

Wheat grain end-use value is determined by complex molecular interactions that occur during grain development, including those in the cell nucleus. However, our knowledge of how the nuclear proteome changes during grain development is limited. Here, we analyzed nuclear proteins of developing wheat grains collected during the cellularization, effective grain-filling, and maturation phases of development, respectively. Nuclear proteins were extracted and separated by two-dimensional gel electrophoresis. Image analysis revealed 371 and 299 reproducible spots in gels with first dimension separation along pH 4-7 and pH 6-11 isoelectric gradients, respectively. The relative abundance of 464 (67%) protein spots changed during grain development. Abundance profiles of these proteins clustered in six groups associated with the major phases and phase transitions of grain development. Using nano liquid chromatography tandem mass spectrometry to analyse 387 variant and non-variant protein spots, 114 different proteins were identified that were classified into 16 functional classes. We noted that some proteins involved in the regulation of transcription, like HMG1/2-like protein and histone deacetylase HDAC2, were most abundant before the phase transition from cellularization to grain-filling, suggesting that major transcriptional changes occur during this key developmental phase. The maturation period was characterized by high relative abundance of proteins involved in ribosome biogenesis. Data are available via ProteomeXchange with identifier PXD002999.

17 alpha-Aminomethyl, 17 alpha-acetamidomethyl, and 17 alpha-hemiglutaramidomethyl derivatives of dihydrotestosterone and testosterone have been prepared by hydrocyanation of 3,3'-(ethylenedioxy)-5 alpha-androstan-17-one and 3,3'-ethylenedioxyandrost-5-en-17-one, reduction of the corresponding acetylated 17 alpha-cyanohydrins with lithium aluminium hydride, and acylation of the resulting 17 alpha-aminomethyl derivatives with either acetic anhydride or the mono acid chloride of glutaric acid mono methyl ester. Saponification of the 17 alpha-hemiglutaramidomethyl methyl esters gave the corresponding hemiglutaramido derivatives, while acid hydrolysis of the 3-ethylene ketal group of 17 alpha-acetamidomethyl and 17 alpha-hemiglutaramidomethyl derivatives regenerated the 3-oxo and 3-oxo-4-ene functions. The 17 alpha-configuration of 17-substituted steroids was determined by 1H and 13C NMR and confirmed by comparing with NMR data for 17 alpha- and 17 beta-cyano-17-hydroxyandrost-4-en-3-one, 17 beta-cyano-3,3'-(ethylenedioxy)androst-5-en-17-ol, 17 alpha-alkynyl, and 17 alpha-hexanoic derivatives of dihydrotestosterone and testosterone, of known 17-configurations. Several ambiguous assignments of 13C NMR signals of 17 alpha-substituted steroids and unsubstituted 17 beta-hydroxy or 17-oxo precursors have been resolved using steroid analogs deuterated at positions C5-7, or C16 for androstane derivatives, and at positions C6-7, or C7 for androstene derivatives. 17 alpha-Aminomethyl and 17 alpha-alkylamidomethyl derivatives of dihydrotestosterone and testosterone are useful intermediates for the access to potential ligands of androgen-binding proteins necessary for affinity chromatography purification or affinity-labeling experiments.

The authors acknowledge Catherine Besson and Jean-Paul Rigaudiere for monitoring of the animal experimentation. We also thank Didier Viala for performing the mass spectrometry analyses at the INRA Clermont-Ferrand/Theix Research Center "Metabolism Exploration Platform: PFEM" and Laetitia Theron for its contribution during mass spectrometry analyses. We acknowledge the Servier library providing pictures for graphical abstract. The project was supported by intramural French National Institute for Agricultural Research (INRA).; Long chain omega 3 polyunsaturated fatty acids (LC-n-3PUFAs) exert potent anti-atherosclerotic action but the mechanisms of action at the vascular level remain unclear. The present study used a non-targeted nutrigenomic approach to investigate the modulations of the aortic proteome in atherosclerotic prone mice following DHA supplementation. LDLR-/- male mice received an atherogenic diet (20 weeks) in parallel with daily oral gavages with either oleic acid-rich oil (Control) or a mixture of oils providing 2% of energy as DHA. The overall protein expression was determined by a proteomic approach followed by bioinformatics analysis. In addition, protein oxidative modifications, namely 4-hydroxynonenal (4-HNE) protein adducts, were detected with a specific antibody followed by MS analysis of the identified spots. Nineteen differentially expressed proteins have been identified in the aorta of the DHA group. The top 5 canonical pathways analysis associated all proteins to metabolic pathways and showed that most of them were related to glucose or lipid metabolism. Up-regulation of superoxide dismutase also suggests an impact of DHA supplementation on vascular antioxidant defenses. The analysis of 4-HNE-protein adducts indicated that DHA supplementation did not enhance oxidative modification of proteins with 4-HNE. This study also identified some new proteins with 4-HNE adducts at the aortic level. In summary, DHA supplementation induces significant modifications of aorta proteome which point out the importance of metabolic changes occurring in the vascular tissue in the presence of LC-n-3PUFAs.

International audience; Fat loss during cooking of duck "foie gras" is the main problem for both manufacturers and consumers. Despite the efforts of the processing industry to control fat loss, the variability of fatty liver cooking yields remains high and uncontrolled. To understand the biochemical effects of postslaughter processing on fat loss during cooking, this study characterizes for the first time the protein expression of fatty liver during chilling using a proteomic approach. For this purpose the proteins were separated according to their solubility: the protein fraction soluble in a buffer of low ionic strength (S) and the protein fraction insoluble in the same buffer (IS). Two-dimensional electrophoresis was used to analyze the S fraction and mass spectrometry for the identification of spots of interest. This analysis revealed 36 (21 identified proteins) and 34 (26 identified proteins) spots of interests in the low-fat-loss and high-fat-loss groups, respectively. The expression of proteins was lower after chilling, which revealed a suppressive effect of chilling on biological processes. The shot-gun strategy was used to analyze the IS fraction, with the identification of all the proteins by mass spectrometry. This allowed identification of 554 and 562 proteins in the low-fat-loss and high-fat-loss groups, respectively. Among these proteins, only the proteins that were up-regulated in the high-fat-loss group were significant (p value = 3.17 X 10(-3)) and corresponded to protein from the cytoskeleton and its associated proteins. Taken together, these results suggest that the variability of technological yield observed in processing plants could be explained by different aging states of fatty livers during chilling, most likely associated with different proteolytic patterns.

International audience; As part of the Sec translocase, the accessory ATPase SecA2 is present in some pathogenic Gram-positive bacteria. In Listeria monocytogenes, deletion of secA2 results in filamentous cells that form rough colonies and have lower virulence. However, only a few proteins have been identified that are secreted by this pathway. This investigation aims to provide the first exoproteomic analysis of the SecA2-dependent secretion in L. monocyto genes EGD-e. By using media and temperatures relevant to bacterial physiology, we demonstrated that the rough colony and elongated bacterial cell morphotypes are highly dependent on growth conditions. Subsequently, comparative exoproteomic analyses of the Delta secA2 versus wt strains were performed in chemically defined medium at 20 degrees C and 37 degrees C. Analyzing the proteomic data following the secretomics-based method, part of the proteins appeared routed towards the Sec pathway and exhibited an N-terminal signal peptide. For another significant part, they were primarily cytoplasmic proteins, thus lacking signal peptide and with no predictable secretion pathway. In total, 13 proteins were newly identified as secreted via SecA2, which were essentially associated with cell-wall metabolism, adhesion and/or biofilm formation. From this comparative exoproteomic analysis, new insights into the L. monocytogenes physiology are discussed in relation to its saprophytic and pathogenic lifestyle

International audience; Meat is an appropriate source of proteins and minerals for human nutrition. Technological treatments modify the physical-chemical properties of proteins, making them liable to decrease the nutritional potential of meat. To counteract this damage, antioxidants and chaperone proteins in muscle cells can prevent oxidation, restore the function of denatured proteins, and thus prevent aggregation. This study aimed to explore the impact of indoor vs outdoor-reared meat protein composition on digestion and to associate protein markers to in vitro digestion parameters. Indoor-reared meat tended to show less oxidation and denaturation than outdoor-reared meat and was characterised by an overexpression of contractile and chaperone proteins. Outdoor-reared meat showed amplification of antioxidant and detoxification metabolism defending against oxidised compounds. Impacts on digestion remained minor. Several protein markers of in vitro digestion parameters were found for aged and cooked meat, linked to the detoxification process and to muscle contraction.

In order to describe developmental changes in human salivary peptidome, whole saliva was obtained from 98 infants followed longitudinally at 3 and 6 months of age. Data on teeth eruption and diet at the age of 6 months were also recorded. Salivary peptide extracts were characterised by label-free MALDI-MS. Peptides differentially expressed between the two ages, and those significantly affected by teeth eruption or introduction of solid foods were identified by MALDI TOF–TOF and LC ESI MS–MS. Out of 81 peaks retained for statistical analysis, 26 were overexpressed at the age of 6 months. Exposure to solid foods had a more pronounced effect on profiles (overexpression of nine peaks) than teeth eruption (overexpression of one peak). Differential peaks corresponded to fragments of acidic and basic PRPs, statherin and histatin. Comparison with existing knowledge on adult saliva peptidome revealed that proteolytic processing of salivary proteins is qualitatively quite comparable in infants and in adults. However, age and diet are modulators of salivary peptidome in human infants.

International audience; We investigated a protein profile evolution during steatosis in ducks using 2-dimensional electrophoresis gels to better understand the mechanisms underlying liver steatosis at the level of hepatic proteins in waterfowl. Two-dimensional electrophoresis gels were performed in the liver at different stages of steatosis in the duck. Mule ducks were slaughtered after 0, 14, or 23 meals of overfeeding, according to commercial conditions. Thirty-one proteic spots were differentially expressed between 3 or 2 durations of overfeeding: 3 spots were differentially expressed between the 3 times and 28 spots were differentially expressed between 2 times. The identified proteins (14) could be regrouped into 5 categories: enzymes, translation factors, proteins involved in cell structure, proteins with antioxidant properties, and proteins that can link calcium. This study opens new research areas in the understanding of steatosis in waterfowl, such as cell structure and oxidative stress.

Chantier qualité GA; In order to identify specific markers of lipid oxidation generated in meat during refrigerated storage and cooking an analysis was conducted to investigate the relationships between the early post-mortem sarcoplasmic proteome, which contains the majority of enzymes involved in the oxidative process, and the level of lipid oxidation. This study was performed in Longissimus lumborum pig muscle. Proteome was analysed by 2-D electrophoresis in combination with liquid chromatography–tandem mass spectrometry (LC–MS/MS) and lipid oxidation was estimated by the TBA reactive substances (TBA-RS) measurement. Many markers of lipid oxidation were identified, but no single marker covered the oxidative process in its entirety. The role of five protein groups (albumin, redoxins, annexins, lipid transporters and enzymes of aerobic respiration), from which a link with lipid oxidation can be established, is discussed. This study, which completes a precedent work focused on protein oxidation, clearly demonstrates that a combination of several markers is needed to assess the sensitivity of meat to oxidation during both ageing and cooking.

Wheat kernel texture, a major trait determining the end-use quality of wheat flour, is mainly influenced by puroindolines. These small basic proteins display in vitro lipid binding and antimicrobial properties, but their cellular functions during grain development remain unknown. To gain an insight into their biological function, a comparative proteome analysis of two near-isogenic lines (NILs) of bread wheat Triticum aestivum L. cv. Falcon differing in the presence or absence of the puroindoline-a gene (Pina) and kernel hardness, was performed. Proteomes of the two NILs were compared at four developmental stages of the grain for the metabolic albumin/globulin fraction and the Triton-extracted amphiphilic fraction. Proteome variations showed that, during grain development, folding proteins and stress-related proteins were more abundant in the hard line compared with the soft one. These results, taken together with ultrastructural observations showing that the formation of the protein matrix occurred earlier in the hard line, suggested that a stress response, possibly the unfolded protein response, is induced earlier in the hard NIL than in the soft one leading to earlier endosperm cell death. Quantification of the albumin/globulin fraction and amphiphilic proteins at each developmental stage strengthened this hypothesis as a plateau was revealed from the 500 degrees Cd stage in the hard NIL whereas synthesis continued in the soft one. These results open new avenues concerning the function of puroindolines which could be involved in the storage protein folding machinery, consequently affecting the development of wheat endosperm and the formation of the protein matrix.

International audience; Fat loss during cooking of duck “foie gras” is the main quality issue for both processors and consumers. Despite the efforts of the processing industry to control fat loss, the variability of fatty liver cooking yield remains high and uncontrolled. To better understand the biological basis of this phenomenon, a proteomic study was conducted. To analyze the protein fraction soluble at low ionic strength (LIS), we used bidimensional electrophoresis and mass spectrometry for the identification of spots of interest. To analyze the protein fraction not soluble at low ionic strength (NS), we used the shotgun strategy. The analysis of data acquired from both protein fractions suggested that at the time of slaughter, livers with low fat loss during cooking were still in anabolic processes with regard to energy metabolism and protein synthesis, whereas livers with high fat loss during cooking developed cell protection mechanisms. The variability in the technological yield observed in processing plants could be explained by a different physiological stage of liver steatosis.

International audience; The cyclization of anticancer drugs into active intermediates has been reported mainly for DNA alkylating molecules including nitrosoureas. We previously defined the original cytotoxic mechanism of anticancerous phenyl '(2-chloroethyl)ureas (CEUs) that involves their reactivity towards cellular proteins and not against DNA; two CEUs subsets have been shown to alkylate β-tubulin and prohibitin leading to inhibition of cell proliferation by G/M or G/S cell cycle arrest. In this study, we demonstrated that cyclic derivatives of CEUs, -phenyl-4,5-dihydrooxazol-2-amines (Oxas) are two to threefold more active than CEUs and share the same cytotoxic properties in B16F0 melanoma cells. Moreover, the CEU original covalent binding by an ester linkage on β-tubulin Glu198 and prohibitin Asp40 was maintained with Oxas. Surprisingly, we observed that Oxas were spontaneously formed from CEUs in the cell culture medium and were also detected within the cells. Our results suggest that the intramolecular cyclization of CEUs leads to active Oxas that should then be considered as the key intermediates for protein alkylation. These results could be useful for the design of new prodrugs for cancer chemotherapy.

Starch is composed of two types of glucose polymers: amylose and amylopectin. The Waxy (Wx) locus controls amylose synthesis in the wheat kernel. Hexaploid wheat has three Wx loci located on chromosomes 7A (Wx-A1), 4A (Wx-B1), and 7D (Wx-D1). Eight near isogenic lines (NILs) of Triticum aestivum cv. Tremie with one, two or three Wx null alleles were used. The albumin–globulin fraction, and amphiphilic proteins were separated using 2-dimensional electrophoresis (2DE) allowing the changes in the waxy kernel to be identified. Albumin–globulin fraction showed overexpression of sucrose synthases in the waxy NILs compared to the normal form of Tremie and a decrease in many proteins related to stress and defence metabolism such as serpins. A subunit of ADP-glucose pyrophosphorylase (AGPase), which is known to play a major role in starch synthesis, was also shown to be down regulated in the waxy NILs. Amphiphilic proteins confirmed the observations made on the albumin–globulin fraction with a decrease in a stress-related protein. These different regulations linked to observations made on wheat kernel (thousand kernel weight (TKW), protein amount per grain, size and distribution of the starch granules) led to formulation of the hypothesis that waxy endosperm does not reach maturity of the wild-type endosperm.

International audience; Oxidative deterioration or modifications of proteins which appear during meat storage and processes can result in the impairment of technological, sensorial and nutritional qualities. Improving the quality involves a better understanding of the biochemical mechanisms responsible for protein oxidation in meat. For that purpose, an analysis was conducted to investigate the relationships between the early post-mortem sarcoplasmic proteome, which contains the majority of enzymes involved in the oxidative process, and protein oxidation generated during meat storage and cooking. This study was performed in Longissimus lumborum pig muscle. In order to have sufficient variability in the proteome and in the meat oxidation level, five groups of 10 animals issued from two different breeds and raised in three different rearing systems were analysed. Protein oxidation was estimated by the measurement of carbonyl groups after 1 and 4 days of refrigerated storage, and after 100 °C experimental cooking of the 4 days aged meat. Significant correlations (p < 0.05) were observed between the level of carbonyl groups and the intensities of 104 spots of the 2D electrophoresis, out of which 52 were clearly identified. The possible involvement of some proteins in the muscle oxidative stress leading to protein oxidation is discussed.

International audience; Objective : The objective of this study was to describe the changes in salivary protein profiles in infants between the ages of 3 and 6 months, and to evaluate the impact of teeth eruption and introduction of solid foods on such profiles. Design : 73 infants were followed longitudinally at 3 and 6 months of age. Their whole saliva proteins were separated by SDS–PAGE electrophoresis and semi-quantified by image analysis. Amylase activity was also measured on a sub-sample of the population (n=42 infants). Bands which abundance was significantly different between the two ages according to paired comparisons were identified by mass spectrometry techniques. Results : Out of 21 bands, 13 were significantly different between 3 and 6 months of age. Two short variants of amylase increased in abundance with age, as did amylase activity. Other changes possibly translated developmental physiological events, for example maturation of the adaptive immune system. The balance between S-type cystatins and cystatins A and B was modified, in favour of S-type cystatins at 6 months of age. Teeth eruption resulted in an increase in albumin abundance, whilst introduction of solid foods was associated with higher levels of beta-2 microglobulin and S-type cystatins. Conclusions : Salivary profiles were modified substantially between the ages of 3 and 6 months. Both teeth eruption and diet had an impact on abundance changes for some proteins, revealing dynamic interactions between saliva proteome, oral physiology and diet.