1
|
Le Bourgot C, Lollier V, Richer Y, Thoulouze L, Svilar L, Le Gall S, Blat S, Le Huërou-Luron I. Maternal short chain fructo-oligosaccharides supplementation during late gestation and lactation influences milk components and offspring gut metabolome: a pilot study. Sci Rep 2024; 14:4236. [PMID: 38378944 PMCID: PMC10879084 DOI: 10.1038/s41598-024-54813-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/16/2024] [Indexed: 02/22/2024] Open
Abstract
Breast milk composition is influenced by maternal diet. This study aimed to evaluate if supplementation of maternal diet with a prebiotic fibre, through its potential effect on milk composition, can be a leverage to orientate the gut microbiota of infants in a way that would be beneficial for their health. Twelve sows received a diet supplemented with short chain fructo-oligosaccharides or maltodextrins during the last month of gestation and the lactation. Oligosaccharidic and lipidomic profiles of colostrum and mature milk (21 days), as well as faecal microbiota composition and metabolomic profile of 21 day-old piglets were evaluated. The total porcine milk oligosaccharide concentration tended to be lower in scFOS-supplemented sows, mainly due to the significant reduction of the neutral core oligosaccharides (in particular that of a tetrahexose). Maternal scFOS supplementation affected the concentration of 31 lipids (mainly long-chain triglycerides) in mature milk. Faecal short-chain fatty acid content and that of 16 bacterial metabolites were modified by scFOS supplementation. Interestingly, the integrative data analysis gave a novel insight into the relationships between (i) maternal milk lipids and PMOs and (ii) offspring faecal bacteria and metabolites. In conclusion, scFOS-enriched maternal diet affected the composition of mature milk, and this was associated with a change in the colonisation of the offspring intestinal microbiota.
Collapse
Affiliation(s)
- Cindy Le Bourgot
- Tereos, Scientific and Regulatory Affairs Department, Moussy-le-Vieux, France.
| | - Virginie Lollier
- INRAE, UR1268 BIA, 44300, Nantes, France
- INRAE, PROBE Research Infrastructure, BIBS Facility, 44300, Nantes, France
| | - Yoann Richer
- INRAE, UR1268 BIA, 44300, Nantes, France
- INRAE, PROBE Research Infrastructure, BIBS Facility, 44300, Nantes, France
| | - Loric Thoulouze
- INRAE, UR1268 BIA, 44300, Nantes, France
- INRAE, PROBE Research Infrastructure, BIBS Facility, 44300, Nantes, France
| | - Ljubica Svilar
- Cribiom, Centre de Recherche Cardiovasculaire et Nutrition C2VN, UMR INRAE 1260 INSERM 1263, University Aix-Marseille, Marseille, France
| | - Sophie Le Gall
- INRAE, UR1268 BIA, 44300, Nantes, France
- INRAE, PROBE Research Infrastructure, BIBS Facility, 44300, Nantes, France
| | - Sophie Blat
- Institut NuMeCan, INRAE, INSERM, University Rennes, 35590, Saint-Gilles, France
| | | |
Collapse
|
2
|
Prunier G, Cherkaoui M, Lysiak A, Langella O, Blein-Nicolas M, Lollier V, Benoist E, Jean G, Fertin G, Rogniaux H, Tessier D. Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides. BMC Bioinformatics 2023; 24:421. [PMID: 37940845 PMCID: PMC10631047 DOI: 10.1186/s12859-023-05555-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND In proteomics, the interpretation of mass spectra representing peptides carrying multiple complex modifications remains challenging, as it is difficult to strike a balance between reasonable execution time, a limited number of false positives, and a huge search space allowing any number of modifications without a priori. The scientific community needs new developments in this area to aid in the discovery of novel post-translational modifications that may play important roles in disease. RESULTS To make progress on this issue, we implemented SpecGlobX (SpecGlob eXTended to eXperimental spectra), a standalone Java application that quickly determines the best spectral alignments of a (possibly very large) list of Peptide-to-Spectrum Matches (PSMs) provided by any open modification search method, or generated by the user. As input, SpecGlobX reads a file containing spectra in MGF or mzML format and a semicolon-delimited spreadsheet describing the PSMs. SpecGlobX returns the best alignment for each PSM as output, splitting the mass difference between the spectrum and the peptide into one or more shifts while considering the possibility of non-aligned masses (a phenomenon resulting from many situations including neutral losses). SpecGlobX is fast, able to align one million PSMs in about 1.5 min on a standard desktop. Firstly, we remind the foundations of the algorithm and detail how we adapted SpecGlob (the method we previously developed following the same aim, but limited to the interpretation of perfect simulated spectra) to the interpretation of imperfect experimental spectra. Then, we highlight the interest of SpecGlobX as a complementary tool downstream to three open modification search methods on a large simulated spectra dataset. Finally, we ran SpecGlobX on a proteome-wide dataset downloaded from PRIDE to demonstrate that SpecGlobX functions just as well on simulated and experimental spectra. We then carefully analyzed a limited set of interpretations. CONCLUSIONS SpecGlobX is helpful as a decision support tool, providing keys to interpret peptides carrying complex modifications still poorly considered by current open modification search software. Better alignment of PSMs enhances confidence in the identification of spectra provided by open modification search methods and should improve the interpretation rate of spectra.
Collapse
Affiliation(s)
- Grégoire Prunier
- INRAE, PROBE Research Infrastructure, BIBS Facility, 44300, Nantes, France
- INRAE, UR1268 Biopolymères Interactions Assemblages, 44316, Nantes, France
| | - Mehdi Cherkaoui
- INRAE, PROBE Research Infrastructure, BIBS Facility, 44300, Nantes, France
- INRAE, UR1268 Biopolymères Interactions Assemblages, 44316, Nantes, France
| | - Albane Lysiak
- INRAE, PROBE Research Infrastructure, BIBS Facility, 44300, Nantes, France
- Nantes Université, CNRS, LS2N, UMR 6004, 44000, Nantes, France
| | - Olivier Langella
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, PAPPSO, 91190, Gif-Sur-Yvette, France
| | - Mélisande Blein-Nicolas
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, PAPPSO, 91190, Gif-Sur-Yvette, France
| | - Virginie Lollier
- INRAE, PROBE Research Infrastructure, BIBS Facility, 44300, Nantes, France
- INRAE, UR1268 Biopolymères Interactions Assemblages, 44316, Nantes, France
| | - Emile Benoist
- Nantes Université, CNRS, LS2N, UMR 6004, 44000, Nantes, France
| | - Géraldine Jean
- Nantes Université, CNRS, LS2N, UMR 6004, 44000, Nantes, France
| | | | - Hélène Rogniaux
- INRAE, PROBE Research Infrastructure, BIBS Facility, 44300, Nantes, France
- INRAE, UR1268 Biopolymères Interactions Assemblages, 44316, Nantes, France
| | - Dominique Tessier
- INRAE, PROBE Research Infrastructure, BIBS Facility, 44300, Nantes, France.
- INRAE, UR1268 Biopolymères Interactions Assemblages, 44316, Nantes, France.
| |
Collapse
|
3
|
Lopez C, David-Briand E, Lollier V, Mériadec C, Bizien T, Pérez J, Artzner F. Solubilization of free β-sitosterol in milk sphingomyelin and polar lipid vesicles as carriers: Structural characterization of the membranes and sphingosome morphology. Food Res Int 2023; 165:112496. [PMID: 36869506 DOI: 10.1016/j.foodres.2023.112496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/29/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023]
Abstract
High consumption of plant sterols reduces the risk of cardiovascular diseases in humans and provides health benefits. Increasing the amount of plant sterols in the diet is therefore necessary to reach the recommended daily dietary intake. However, food supplementation with free plant sterols is challenging because of their low solubility in fats and water. The objectives of this study were to investigate the capacity of milk-sphingomyelin (milk-SM) and milk polar lipids to solubilise β-sitosterol molecules in bilayer membranes organised as vesicles called sphingosomes. The thermal and structural properties of milk-SM containing bilayers composed of various amounts of β-sitosterol were examined by differential scanning calorimetry (DSC) and temperature-controlled X-ray diffraction (XRD), the molecular interactions were studied using the Langmuir film technique, the morphologies of sphingosomes and β-sitosterol crystals were observed by microscopy. We showed that the milk-SM bilayers devoid of β-sitosterol exhibited a gel to fluid Lα phase transition for Tm = 34.5 °C and formed facetted spherical sphingosomes below Tm. The solubilisation of β-sitosterol within milk-SM bilayers induced a liquid-ordered Lo phaseabove 25 %mol (1.7 %wt) β-sitosterol and a softening of the membranes leading to the formation of elongated sphingosomes. Attractive molecular interactions revealed a condensing effect of β-sitosterol on milk-SM Langmuir monolayers. Above 40 %mol (25.7 %wt) β-sitosterol, partitioning occured with the formation of β-sitosterol microcrystals in the aqueous phase. Similar results were obtained with the solubilization of β-sitosterol within milk polar lipid vesicles. For the first time, this study highlighted the efficient solubilization of free β-sitosterol within milk-SM based vesicles, which opens new market opportunities for the formulation of functional foods enriched in non-crystalline free plant sterols.
Collapse
Affiliation(s)
- Christelle Lopez
- INRAE, BIA, F-44316 Nantes, France; INRAE, STLO, F-35000 Rennes, France.
| | | | - Virginie Lollier
- INRAE, BIA, F-44316 Nantes, France; INRAE, PROBE Research Infrastructure, BIBS Facility, F-44316 Nantes, France
| | | | - Thomas Bizien
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin BP48, F-91192 Gif-sur-Yvette, France
| | - Javier Pérez
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin BP48, F-91192 Gif-sur-Yvette, France
| | - Franck Artzner
- IPR, UMR 6251, CNRS, University of Rennes 1, F-35042 Rennes, France
| |
Collapse
|
4
|
Mameri H, Gaudin JC, Lollier V, Tranquet O, Brossard C, Pietri M, Marion D, Codreanu-Morel F, Beaudouin E, Wien F, Gohon Y, Briozzo P, Denery-Papini S. Critical structural elements for the antigenicity of wheat allergen LTP1 (Tri a 14) revealed by site-directed mutagenesis. Sci Rep 2022; 12:12253. [PMID: 35851276 PMCID: PMC9293932 DOI: 10.1038/s41598-022-15811-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/29/2022] [Indexed: 11/09/2022] Open
Abstract
Lipid transfer proteins (LTPs) were identified as allergens in a large variety of pollens and foods, including cereals. LTPs belong to the prolamin superfamily and display an α-helical fold, with a bundle of four α-helices held together by four disulfide bonds. Wheat LTP1 is involved in allergic reactions to food. To identify critical structural elements of antibody binding to wheat LTP1, we used site-directed mutagenesis on wheat recombinant LTP1 to target: (i) sequence conservation and/or structure flexibility or (ii) each disulfide bond. We evaluated the modifications induced by these mutations on LTP1 secondary structure by synchrotron radiation circular dichroism and on its antigenicity with patient's sera and with mouse monoclonal antibodies. Disruption of the C28-C73 disulfide bond significantly affected IgE-binding and caused protein denaturation, while removing C13-C27 bond decreased LTP1 antigenicity and slightly modified LTP1 overall folding. In addition, we showed Lys72 to be a key residue; the K72A mutation did not affect global folding but modified the local 3D structure of LTP1 and strongly reduced IgE-binding. This work revealed a cluster of residues (C13, C27, C28, C73 and K72), four of which embedded in disulfide bonds, which play a critical role in LTP1 antigenicity.
Collapse
Affiliation(s)
- Hamza Mameri
- INRAE, UR 1268 Biopolymères Interactions Assemblages (BIA), 44316, Nantes, France. .,UMR 1208 IATE, Univ Montpellier, INRAE, L'Institut-Agro Montpellier, 34060, Montpellier, France.
| | - Jean-Charles Gaudin
- INRAE, UR 1268 Biopolymères Interactions Assemblages (BIA), 44316, Nantes, France.,INRAE, UMR 0588 Biologie intégrée pour la valorisation de la diversité des arbres et de la forêt (BIOFORA), 45075, Orléans, France
| | - Virginie Lollier
- INRAE, UR 1268 Biopolymères Interactions Assemblages (BIA), 44316, Nantes, France.,INRAE, UR BIA, 44316, Nantes, France.,INRAE, PROBE Research Infrastructure, BIBS Facility, 44316, Nantes, France
| | - Olivier Tranquet
- INRAE, UR 1268 Biopolymères Interactions Assemblages (BIA), 44316, Nantes, France.,INRAE UMR 1163 Biodiversité et Biotechnologie Fongiques (BBF), 13288, Marseille, France
| | - Chantal Brossard
- INRAE, UR 1268 Biopolymères Interactions Assemblages (BIA), 44316, Nantes, France
| | - Manon Pietri
- INRAE, UR 1268 Biopolymères Interactions Assemblages (BIA), 44316, Nantes, France.,Institut de Cancérologie de l'Ouest, Centre René Gauducheau, 44805, Saint Herblain Cedex, France
| | - Didier Marion
- INRAE, UR 1268 Biopolymères Interactions Assemblages (BIA), 44316, Nantes, France
| | - Fanny Codreanu-Morel
- CHU Luxembourg, Centre Hospitalier de Luxembourg, Kanner Klinik, 1210, Luxembourg, Luxembourg
| | - Etienne Beaudouin
- Service d'Allergologie, Hôpital de Mercy, CHR Metz, 57000, Metz, France
| | - Frank Wien
- Synchrotron Soleil, Saint-Aubin, 91192, Gif-sur-Yvette, France
| | - Yann Gohon
- INRAE, UMR 1318 Institut Jean-Pierre Bourgin, 78026, Versailles, France
| | - Pierre Briozzo
- INRAE, UMR 1318 Institut Jean-Pierre Bourgin, 78026, Versailles, France
| | - Sandra Denery-Papini
- INRAE, UR 1268 Biopolymères Interactions Assemblages (BIA), 44316, Nantes, France.
| |
Collapse
|
5
|
Cherkaoui M, Tessier D, Lollier V, Larre C, Brossard C, Dijk W, Rogniaux H. High-resolution mass spectrometry unveils the molecular changes of ovalbumin induced by heating and their influence on IgE binding capacity. Food Chem 2022; 395:133624. [DOI: 10.1016/j.foodchem.2022.133624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 11/26/2022]
|
6
|
Lollier V, Fanuel M, Ropartz D, Tessier D, Rogniaux H. Oligator: a flexible interface to draw oligosaccharide structures and generate their theoretical tandem mass spectra. Bioinformatics 2021; 37:4261-4262. [PMID: 34050747 DOI: 10.1093/bioinformatics/btab412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/22/2021] [Accepted: 05/27/2021] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Oligator is software designed to assist scientists in their exploration of MS/MS experiments, especially for oligosaccharides bearing unreferenced chemical substitutions. Through a graphical interface, users have the total flexibility to build a candidate glycan structure and produce the corresponding theoretical MS/MS spectrum in accordance with the usual ion nomenclature. The structural information is saved using standard notations, in text format, which facilitates the capitalization and exchange of data as well as any other processing of the information. AVAILABILITY Source code and user manual are freely available at https://github.com/vlollier/oligator. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Virginie Lollier
- INRAE, UR BIA, Nantes, F-44316, France.,INRAE, PROBE research infrastructure, BIBS facility, Nantes, F-44316, France
| | - Mathieu Fanuel
- INRAE, UR BIA, Nantes, F-44316, France.,INRAE, PROBE research infrastructure, BIBS facility, Nantes, F-44316, France
| | - David Ropartz
- INRAE, UR BIA, Nantes, F-44316, France.,INRAE, PROBE research infrastructure, BIBS facility, Nantes, F-44316, France
| | - Dominique Tessier
- INRAE, UR BIA, Nantes, F-44316, France.,INRAE, PROBE research infrastructure, BIBS facility, Nantes, F-44316, France
| | - Hélène Rogniaux
- INRAE, UR BIA, Nantes, F-44316, France.,INRAE, PROBE research infrastructure, BIBS facility, Nantes, F-44316, France
| |
Collapse
|
7
|
Cherkaoui M, Geairon A, Lollier V, Clemente HS, Larré C, Rogniaux H, Jamet E, Guillon F, Francin-Allami M. Cell Wall Proteome Investigation of Bread Wheat (Triticum Aestivum) Developing Grain in Endosperm and Outer Layers. Proteomics 2018; 18:e1800286. [PMID: 30288912 DOI: 10.1002/pmic.201800286] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/13/2018] [Indexed: 12/29/2022]
Abstract
The remodeling of cell wall polysaccharides is controlled by cell wall proteins (CWPs) during the development of wheat grain. This work describes for the first time the cell wall proteomes of the endosperm and outer layers of the wheat developing grain, which have distinct physiological functions and technological uses. Altogether 636 nonredundant predicted CWPs are identified with 337 proteins in the endosperm and 594 proteins in the outer layers, among which 295 proteins are present in both tissues, suggesting both common and tissue specific remodeling activities. These proteins are distributed into eight functional classes. Approximatively a quarter of them were predicted to act on cell wall polysaccharides, with many glycosylhydrolases and also expansin, lyases, and carbohydrate esterases. Therefore, these results provide crucial data to go further in the understanding of relationship between tissue-specific morphogenesis and cell wall remodeling in cereals. Data are available via ProteomeXchange with identifier PXD010367.
Collapse
Affiliation(s)
| | - Audrey Geairon
- INRA, Biopolymères Interactions Assemblages, Nantes, France
| | | | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, Auzeville, Castanet Tolosan, France
| | - Colette Larré
- INRA, Biopolymères Interactions Assemblages, Nantes, France
| | | | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, Auzeville, Castanet Tolosan, France
| | | | | |
Collapse
|
8
|
Abstract
Several proteomic database search engines that interpret LC-MS/MS data do not identify the same set of peptides. These disagreements occur even when the scores of the peptide-to-spectrum matches suggest good confidence in the interpretation. Our study shows that these disagreements observed for the interpretations of a given spectrum are almost exclusively due to the variation of what we call the "peptide space", i.e., the set of peptides that are actually compared to the experimental spectra. We discuss the potential difficulties of precisely defining the "peptide space." Indeed, although several parameters that are generally reported in publications can easily be set to the same values, many additional parameters-with much less straightforward user access-might impact the "peptide space" used by each program. Moreover, in a configuration where each search engine identifies the same candidates for each spectrum, the inference of the proteins may remain quite different depending on the false discovery rate selected.
Collapse
Affiliation(s)
- Dominique Tessier
- INRA, UR 1268 Biopolymères Interactions Assemblages, F-44300 Nantes, France
| | - Virginie Lollier
- INRA, UR 1268 Biopolymères Interactions Assemblages, F-44300 Nantes, France
| | - Colette Larré
- INRA, UR 1268 Biopolymères Interactions Assemblages, F-44300 Nantes, France
| | - Hélène Rogniaux
- INRA, UR 1268 Biopolymères Interactions Assemblages, F-44300 Nantes, France
| |
Collapse
|
9
|
Francin-Allami M, Lollier V, Pavlovic M, San Clemente H, Rogniaux H, Jamet E, Guillon F, Larré C. Understanding the Remodelling of Cell Walls during Brachypodium distachyon Grain Development through a Sub-Cellular Quantitative Proteomic Approach. Proteomes 2016; 4:E21. [PMID: 28248231 PMCID: PMC5217356 DOI: 10.3390/proteomes4030021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/16/2016] [Accepted: 06/20/2016] [Indexed: 12/18/2022] Open
Abstract
Brachypodiumdistachyon is a suitable plant model for studying temperate cereal crops, such as wheat, barley or rice, and helpful in the study of the grain cell wall. Indeed, the most abundant hemicelluloses that are in the B. distachyon cell wall of grain are (1-3)(1-4)-β-glucans and arabinoxylans, in a ratio similar to those of cereals such as barley or oat. Conversely, these cell walls contain few pectins and xyloglucans. Cell walls play an important role in grain physiology. The modifications of cell wall polysaccharides that occur during grain development and filling are key in the determination of the size and weight of the cereal grains. The mechanisms required for cell wall assembly and remodelling are poorly understood, especially in cereals. To provide a better understanding of these processes, we purified the cell wall at three developmental stages of the B. distachyon grain. The proteins were then extracted, and a quantitative and comparative LC-MS/MS analysis was performed to investigate the protein profile changes during grain development. Over 466 cell wall proteins (CWPs) were identified and classified according to their predicted functions. This work highlights the different proteome profiles that we could relate to the main phases of grain development and to the reorganization of cell wall polysaccharides that occurs during these different developmental stages. These results provide a good springboard to pursue functional validation to better understand the role of CWPs in the assembly and remodelling of the grain cell wall of cereals.
Collapse
Affiliation(s)
| | - Virginie Lollier
- UR1268 BIA (Biopolymères Interactions Assemblages), INRA, Nantes 44300, France.
| | - Marija Pavlovic
- UR1268 BIA (Biopolymères Interactions Assemblages), INRA, Nantes 44300, France.
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 Chemin de Borderouge-Auzeville, BP42617, Castanet-Tolosan 31326, France.
| | - Hélène Rogniaux
- UR1268 BIA (Biopolymères Interactions Assemblages), INRA, Nantes 44300, France.
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 Chemin de Borderouge-Auzeville, BP42617, Castanet-Tolosan 31326, France.
| | - Fabienne Guillon
- UR1268 BIA (Biopolymères Interactions Assemblages), INRA, Nantes 44300, France.
| | - Colette Larré
- UR1268 BIA (Biopolymères Interactions Assemblages), INRA, Nantes 44300, France.
| |
Collapse
|
10
|
Rogniaux H, Pavlovic M, Lupi R, Lollier V, Joint M, Mameri H, Denery S, Larré C. Allergen relative abundance in several wheat varieties as revealed via a targeted quantitative approach using MS. Proteomics 2016; 15:1736-45. [PMID: 25764008 DOI: 10.1002/pmic.201400416] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 02/13/2015] [Accepted: 03/02/2015] [Indexed: 12/18/2022]
Abstract
Food allergy has become a major health issue in developed countries, therefore there is an urgent need to develop analytical methods able to detect and quantify with a good sensitivity and reliability some specific allergens in complex food matrices. In this paper, we present a targeted MS/MS approach to compare the relative abundance of the major recognized wheat allergens in the salt-soluble (albumin/globulin) fraction of wheat grains. Twelve allergens were quantified in seven wheat varieties, selected from three Triticum species: T. aestivum (bread wheat), T. durum (durum wheat), and T. monococcum. The allergens were monitored from one or two proteotypic peptides and their relative abundance was deduced from the intensity of one fragment measured in MS/MS. Whereas the abundance of some of the targeted allergens was quite stable across the genotypes, others like alpha-amylase inhibitors showed clear differences according to the wheat species, in accordance with the results of earlier functional studies. This study enriches the scarce knowledge available on allergens content in wheat genotypes, and brings new perspectives for food safety and plant breeding.
Collapse
Affiliation(s)
- Hélène Rogniaux
- INRA UR1268 Biopolymers Interactions Assemblies, Nantes, France
| | - Marija Pavlovic
- INRA UR1268 Biopolymers Interactions Assemblies, Nantes, France
| | - Roberta Lupi
- INRA UR1268 Biopolymers Interactions Assemblies, Nantes, France
| | | | - Mathilde Joint
- INRA UR1268 Biopolymers Interactions Assemblies, Nantes, France
| | - Hamza Mameri
- INRA UR1268 Biopolymers Interactions Assemblies, Nantes, France
| | - Sandra Denery
- INRA UR1268 Biopolymers Interactions Assemblies, Nantes, France
| | - Colette Larré
- INRA UR1268 Biopolymers Interactions Assemblies, Nantes, France
| |
Collapse
|
11
|
Chateigner-Boutin AL, Suliman M, Bouchet B, Alvarado C, Lollier V, Rogniaux H, Guillon F, Larré C. Endomembrane proteomics reveals putative enzymes involved in cell wall metabolism in wheat grain outer layers. J Exp Bot 2015; 66:2649-58. [PMID: 25769308 PMCID: PMC4986875 DOI: 10.1093/jxb/erv075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Cereal grain outer layers fulfil essential functions for the developing seed such as supplying energy and providing protection. In the food industry, the grain outer layers called 'the bran' is valuable since it is rich in dietary fibre and other beneficial nutriments. The outer layers comprise several tissues with a high content in cell wall material. The cell wall composition of the grain peripheral tissues was investigated with specific probes at a stage of active cell wall synthesis. Considerable wall diversity between cell types was revealed. To identify the cellular machinery involved in cell wall synthesis, a subcellular proteomic approach was used targeting the Golgi apparatus where most cell wall polysaccharides are synthesized. The tissues were dissected into outer pericarp and intermediate layers where 822 and 1304 proteins were identified respectively. Many carbohydrate-active enzymes were revealed: some in the two peripheral grain fractions, others only in one tissue. Several protein families specific to one fraction and with characterized homologs in other species might be related to the specific detection of a polysaccharide in a particular cell layer. This report provides new information on grain cell walls and its biosynthesis in the valuable outer tissues, which are poorly studied so far. A better understanding of the mechanisms controlling cell wall composition could help to improve several quality traits of cereal products (e.g. dietary fibre content, biomass conversion to biofuel).
Collapse
Affiliation(s)
| | - Muhtadi Suliman
- INRA, UR1268 Biopolymères, Interactions Assemblages, F-44316 Nantes, France
| | - Brigitte Bouchet
- INRA, UR1268 Biopolymères, Interactions Assemblages, F-44316 Nantes, France
| | - Camille Alvarado
- INRA, UR1268 Biopolymères, Interactions Assemblages, F-44316 Nantes, France
| | - Virginie Lollier
- INRA, UR1268 Biopolymères, Interactions Assemblages, F-44316 Nantes, France
| | - Hélène Rogniaux
- INRA, UR1268 Biopolymères, Interactions Assemblages, F-44316 Nantes, France
| | - Fabienne Guillon
- INRA, UR1268 Biopolymères, Interactions Assemblages, F-44316 Nantes, France
| | - Colette Larré
- INRA, UR1268 Biopolymères, Interactions Assemblages, F-44316 Nantes, France
| |
Collapse
|
12
|
Francin-Allami M, Merah K, Albenne C, Rogniaux H, Pavlovic M, Lollier V, Sibout R, Guillon F, Jamet E, Larré C. Cell wall proteomic of Brachypodium distachyon grains: A focus on cell wall remodeling proteins. Proteomics 2015; 15:2296-306. [PMID: 25787258 DOI: 10.1002/pmic.201400485] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 01/23/2015] [Accepted: 03/13/2015] [Indexed: 01/12/2023]
Abstract
Cell walls play key roles during plant development. Following their deposition into the cell wall, polysaccharides are continually remodeled according to the growth stage and stress environment to accommodate cell growth and differentiation. To date, little is known concerning the enzymes involved in cell wall remodeling, especially in gramineous and particularly in the grain during development. Here, we investigated the cell wall proteome of the grain of Brachypodium distachyon. This plant is a suitable model for temperate cereal crops. Among the 601 proteins identified, 299 were predicted to be secreted. These proteins were distributed into eight functional classes; the class of proteins that act on carbohydrates was the most highly represented. Among these proteins, numerous glycoside hydrolases were found. Expansins and peroxidases, which are assumed to be involved in cell wall polysaccharide remodeling, were also identified. Approximately half of the proteins identified in this study were newly discovered in grain and were not identified in the previous proteome analysis conducted using the culms and leaves of B. distachyon. Therefore, the data obtained from all organs of B. distachyon infer a global cell wall proteome consisting of 460 proteins. At present, this is the most extensive cell wall proteome of a monocot species.
Collapse
Affiliation(s)
| | - Kahina Merah
- INRA, Biopolymères Interactions Assemblages, Nantes, France.,Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Castanet-Tolosan, France.,CNRS, Castanet-Tolosan, France
| | - Cécile Albenne
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Castanet-Tolosan, France.,CNRS, Castanet-Tolosan, France
| | | | | | | | - Richard Sibout
- INRA, Institut Jean-Pierre Bourgin (IJPB), Saclay Plant Science, Versailles, France
| | | | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Castanet-Tolosan, France.,CNRS, Castanet-Tolosan, France
| | - Colette Larré
- INRA, Biopolymères Interactions Assemblages, Nantes, France
| |
Collapse
|
13
|
Denery-Papini S, Lollier V, Mameri H, Pietri M, Larre C, Gaudin JC, Tranquet O, Drouet M, Paty E, Jonathan AM, Beaudouin E, Moneret-Vautrin AD, Tessier D. In silico prediction of B cell epitopes and experimental validation on wheat allergens. Clin Transl Allergy 2014. [PMCID: PMC4072010 DOI: 10.1186/2045-7022-4-s2-o4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
14
|
Lollier V, Denery-Papini S, Larré C, Tessier D. A generic approach to evaluate how B-cell epitopes are surface-exposed on protein structures. Mol Immunol 2010; 48:577-85. [PMID: 21111484 PMCID: PMC7112657 DOI: 10.1016/j.molimm.2010.10.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 10/24/2010] [Indexed: 11/17/2022]
Abstract
Methods that predict antibody epitopes could help to promote the development of diagnostic tools, vaccines or immunotherapies by affecting the epitope binding of antibodies during an immunological response to antigens. It is generally assumed that there is a direct relationship between antibody accessibility to antigens and accessible surface of proteins. Based on this assumption, prediction systems often includes solvent accessibility values calculated from the primary sequence of proteins or from their three dimensional structures as a predictive criterion. However, the current prediction systems seem weakly efficient in view of benchmark tests. We were interested in evaluating how amino acids that have been experimentally identified as epitopic elements could differ from the rest of the antigenic molecule at the level of surface exposure, hence we assessed the average accessibility of epitopes. The approach used here utilises published epitopes deduced from numerous identification techniques, including sequence scanning and structure visualisation after crystallography, and it involves many types of antigens from toxins to allergens. Our results show that epitopic residues are not distributed among any specific Relative Surface Accessibility and Protrusion Index values and that, in some cases, epitopes cover the entire antigenic sequence. These results led to the conclusion that the classification of known epitopes with respect to the experimental conditions used to identify them should be introduced before attempting to characterise epitopic areas in a generic way.
Collapse
Affiliation(s)
- Virginie Lollier
- UR1268 Biopolymers, Interactions, Assemblies, INRA, 44300 Nantes, France.
| | | | | | | |
Collapse
|
15
|
Larré C, Penninck S, Bouchet B, Lollier V, Tranquet O, Denery-Papini S, Guillon F, Rogniaux H. Brachypodium distachyon grain: identification and subcellular localization of storage proteins. J Exp Bot 2010; 61:1771-83. [PMID: 20385545 PMCID: PMC2852671 DOI: 10.1093/jxb/erq050] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 01/28/2010] [Accepted: 02/10/2010] [Indexed: 05/19/2023]
Abstract
Seed storage proteins are of great importance in nutrition and in industrial transformation because of their functional properties. Brachypodium distachyon has been proposed as a new model plant to study temperate cereals. The protein composition of Brachypodium grain was investigated by separating the proteins on the basis of their solubility combined with a proteomic approach. Salt-soluble proteins as well as salt-insoluble proteins separated by two-dimensional gel electrophoresis revealed 284 and 120 spots, respectively. Proteins from the major spots were sequenced by mass spectrometry and identified by searching against a Brachypodium putative protein database. Our analysis detected globulins and prolamins but no albumins. Globulins were represented mainly by the 11S type and their solubility properties corresponded to the glutelin found in rice. An in silico search for storage proteins returned more translated genes than expressed products identified by mass spectrometry, particularly in the case of prolamin type proteins, reflecting a strong expression of globulins at the expense of prolamins. Microscopic examination of endosperm cells revealed scarce small-size starch granules surrounded by protein bodies containing 11S globulins. The presence of protein bodies containing glutelins makes B. distachyon closer to rice or oat than to wheat endosperm.
Collapse
Affiliation(s)
- C Larré
- UR1268 Biopolymères Interactions Assemblages, INRA, F-44300 Nantes, France.
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Fargette M, Lollier V, Phillips M, Blok V, Frutos R. AFLP analysis of the genetic diversity of Meloidogyne chitwoodi and M. fallax, major agricultural pests. C R Biol 2005; 328:455-62. [PMID: 15948634 DOI: 10.1016/j.crvi.2005.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
M. chitwoodi and M. fallax populations are clustered and separated from the other species studied. The genetic diversity observed for M. incognita, M. arenaria, M. javanica, M. hapla, and M. mayaguensis correlates well with the previously validated species. Two main groups can be identified within the M. chitwoodi/M. fallax cluster, the first group comprises only M. chitwoodi populations whereas the second group is made of M. chitwoodi and M. fallax populations. Moreover, M. chitwoodi displays a higher genetic diversity than M. fallax and is characterised by the presence of several clusters.
Collapse
Affiliation(s)
- Mireille Fargette
- IRD, UMR-CBGP, Campus international de Baillarguet, CS30016, 34988 Montferrier-sur-Lez, France.
| | | | | | | | | |
Collapse
|