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Suwareh O, Causeur D, Le Feunteun S, Jardin J, Briard-Bion V, Pezennec S, Nau F. Peptide bonds cleaved by pepsin are affected by the morphology of heat-induced ovalbumin aggregates. Food Chem 2024; 458:140260. [PMID: 38944927 DOI: 10.1016/j.foodchem.2024.140260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 07/02/2024]
Abstract
The study aimed to assess the extent to which protein aggregation, and even the modality of aggregation, can affect gastric digestion, down to the nature of the hydrolyzed peptide bonds. By controlling pH and ionic strength during heating, linear or spherical ovalbumin (OVA) aggregates were prepared, then digested with pepsin. Statistical analysis characterized the peptide bonds specifically hydrolyzed versus those not hydrolyzed for a given condition, based on a detailed description of all these bonds. Aggregation limits pepsin access to buried regions of native OVA, but some cleavage sites specific to aggregates reflect specific hydrolysis pathways due to the denaturation-aggregation process. Cleavage sites specific to linear aggregates indicate greater denaturation compared to spherical aggregates, consistent with theoretical models of heat-induced aggregation of OVA. Thus, the peptides released during the gastric phase may vary depending on the aggregation modality. Precisely tuned aggregation may therefore allow subtle control of the digestion process.
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Affiliation(s)
- Ousmane Suwareh
- STLO, INRAE, Institut Agro, 65 rue de Saint-Brieuc, 35042 Rennes, France.
| | - David Causeur
- IRMAR UMR6625, CNRS, Institut Agro, 65 rue de Saint-Brieuc, 35042 Rennes, France.
| | - Steven Le Feunteun
- STLO, INRAE, Institut Agro, 65 rue de Saint-Brieuc, 35042 Rennes, France.
| | - Julien Jardin
- STLO, INRAE, Institut Agro, 65 rue de Saint-Brieuc, 35042 Rennes, France.
| | | | - Stéphane Pezennec
- STLO, INRAE, Institut Agro, 65 rue de Saint-Brieuc, 35042 Rennes, France.
| | - Françoise Nau
- STLO, INRAE, Institut Agro, 65 rue de Saint-Brieuc, 35042 Rennes, France.
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2
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Freitas ADS, Barroso FAL, Campos GM, Américo MF, Viegas RCDS, Gomes GC, Vital KD, Fernandes SOA, Carvalho RDDO, Jardin J, Miranda APGDS, Ferreira E, Martins FS, Laguna JG, Jan G, Azevedo V, de Jesus LCL. Exploring the anti-inflammatory effects of postbiotic proteins from Lactobacillus delbrueckii CIDCA 133 on inflammatory bowel disease model. Int J Biol Macromol 2024; 277:134216. [PMID: 39069058 DOI: 10.1016/j.ijbiomac.2024.134216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024]
Abstract
Lactobacillus delbrueckii CIDCA 133 is a promising health-promoting bacterium shown to alleviate intestinal inflammation. However, the specific bacterial components responsible for these effects remain largely unknown. Here, we demonstrated that consuming extractable proteins from the CIDCA 133 strain effectively relieved acute ulcerative colitis in mice. This postbiotic protein fraction reduced the disease activity index and prevented colon shortening in mice. Furthermore, histological analysis revealed colitis prevention with reduced inflammatory cell infiltration into the colon mucosa. Postbiotic consumption also induced an immunomodulatory profile in colitic mice, as evidenced by both mRNA transcript levels (Tlr2, Nfkb1, Nlpr3, Tnf, and Il6) and cytokines concentration (IL1β, TGFβ, and IL10). Additionally, it enhanced the levels of secretory IgA, upregulated the transcript levels of tight junction proteins (Hp and F11r), and improved paracellular intestinal permeability. More interestingly, the consumption of postbiotic proteins modulated the gut microbiota (Bacteroides, Arkkemansia, Dorea, and Oscillospira). Pearson correlation analysis indicated that IL10 and IL1β levels were positively associated with Bacteroides and Arkkemansia_Lactobacillus abundance. Our study reveals that CIDCA 133-derived proteins possess anti-inflammatory properties in colonic inflammation.
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Affiliation(s)
- Andria Dos Santos Freitas
- Federal University of Minas Gerais, Department of Genetics, Ecology, and Evolution, Belo Horizonte, Minas Gerais, Brazil
| | | | - Gabriela Munis Campos
- Federal University of Minas Gerais, Department of Genetics, Ecology, and Evolution, Belo Horizonte, Minas Gerais, Brazil
| | - Monique Ferrary Américo
- Federal University of Minas Gerais, Department of Genetics, Ecology, and Evolution, Belo Horizonte, Minas Gerais, Brazil
| | | | - Gabriel Camargos Gomes
- Federal University of Minas Gerais, Department of Genetics, Ecology, and Evolution, Belo Horizonte, Minas Gerais, Brazil
| | - Kátia Duarte Vital
- Federal University of Minas Gerais, Department of Clinical and Toxicological Analysis, Belo Horizonte, Minas Gerais, Brazil
| | | | | | | | | | - Enio Ferreira
- Federal University of Minas Gerais, Department of General Pathology, Belo Horizonte, Minas Gerais, Brazil
| | - Flaviano Santos Martins
- Federal University of Minas Gerais, Department of Microbiology, Belo Horizonte, Minas Gerais, Brazil
| | - Juliana Guimarães Laguna
- Federal University of Minas Gerais, Department of Genetics, Ecology, and Evolution, Belo Horizonte, Minas Gerais, Brazil
| | | | - Vasco Azevedo
- Federal University of Minas Gerais, Department of Genetics, Ecology, and Evolution, Belo Horizonte, Minas Gerais, Brazil.
| | - Luís Cláudio Lima de Jesus
- Federal University of Minas Gerais, Department of Genetics, Ecology, and Evolution, Belo Horizonte, Minas Gerais, Brazil.
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3
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Giribaldi M, Nebbia S, Briard-Bion V, Jardin J, Ménard O, Dupont D, Coscia A, Cresi F, Lamberti C, Cavallarin L, Deglaire A. Peptidomic profile of human milk as influenced by fortification with different protein sources: An in vitro dynamic digestion simulation. Food Chem 2024; 462:140886. [PMID: 39213965 DOI: 10.1016/j.foodchem.2024.140886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 08/02/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
Fortification of human milk (HM) is often necessary to meet the nutritional requirements of preterm infants. The present experiment aimed to establish whether the supplementation of HM with either an experimental donkey milk-derived fortifier containing whole donkey milk proteins, or with a commercial bovine milk-derived fortifier containing hydrolyzed bovine whey proteins, affects peptide release differently during digestion. The experiment was conducted using an in vitro dynamic system designed to simulate the preterm infant's digestion followed by digesta analysis by means of LC-MS-MS. The different fortifiers did not appear to influence the cumulative intensity of HM peptides. Fortification had a differential impact on the release of either donkey or bovine bioactive peptides. Donkey milk peptides showed antioxidant/ACE inhibitory activities, while bovine peptides showed opioid, dipeptil- and propyl endo- peptidase inhibitory and antimicrobial activity. A slight delay in peptide release from human lactoferrin and α-lactalbumin was observed when HM was supplemented with donkey milk-derived fortifier.
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Affiliation(s)
- Marzia Giribaldi
- CNR Institute of Sciences of Food Production, Largo Braccini 2, 10095 Grugliasco, TO, Italy.
| | - Stefano Nebbia
- CNR Institute of Sciences of Food Production, Largo Braccini 2, 10095 Grugliasco, TO, Italy; INRAE, L'Institut Agro, Science et Technologie du Lait et de l'Oeuf, 65 Rue de St Brieuc, 35042 Rennes, France
| | - Valerie Briard-Bion
- INRAE, L'Institut Agro, Science et Technologie du Lait et de l'Oeuf, 65 Rue de St Brieuc, 35042 Rennes, France.
| | - Julien Jardin
- INRAE, L'Institut Agro, Science et Technologie du Lait et de l'Oeuf, 65 Rue de St Brieuc, 35042 Rennes, France.
| | - Olivia Ménard
- INRAE, L'Institut Agro, Science et Technologie du Lait et de l'Oeuf, 65 Rue de St Brieuc, 35042 Rennes, France.
| | - Didier Dupont
- INRAE, L'Institut Agro, Science et Technologie du Lait et de l'Oeuf, 65 Rue de St Brieuc, 35042 Rennes, France.
| | - Alessandra Coscia
- Neonatal Unit, University of Turin, City of Health and Science of Turin, via Ventimiglia 3, 10126 Turin, Italy.
| | - Francesco Cresi
- Neonatal Unit, University of Turin, City of Health and Science of Turin, via Ventimiglia 3, 10126 Turin, Italy.
| | - Cristina Lamberti
- CNR Institute of Sciences of Food Production, Largo Braccini 2, 10095 Grugliasco, TO, Italy.
| | - Laura Cavallarin
- CNR Institute of Sciences of Food Production, Largo Braccini 2, 10095 Grugliasco, TO, Italy.
| | - Amélie Deglaire
- INRAE, L'Institut Agro, Science et Technologie du Lait et de l'Oeuf, 65 Rue de St Brieuc, 35042 Rennes, France.
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4
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Langella O, Renne T, Balliau T, Davanture M, Brehmer S, Zivy M, Blein-Nicolas M, Rusconi F. Full Native timsTOF PASEF-Enabled Quantitative Proteomics with the i2MassChroQ Software Package. J Proteome Res 2024; 23:3353-3366. [PMID: 39016325 DOI: 10.1021/acs.jproteome.3c00732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Ion mobility mass spectrometry has become popular in proteomics lately, in particular because the Bruker timsTOF instruments have found significant adoption in proteomics facilities. The Bruker's implementation of the ion mobility dimension generates massive amounts of mass spectrometric data that require carefully designed software both to extract meaningful information and to perform processing tasks at reasonable speed. In a historical move, the Bruker company decided to harness the skills of the scientific software development community by releasing to the public the timsTOF data file format specification. As a proteomics facility that has been developing Free Open Source Software (FOSS) solutions since decades, we took advantage of this opportunity to implement the very first FOSS proteomics complete solution to natively read the timsTOF data, low-level process them, and explore them in an integrated quantitative proteomics software environment. We dubbed our software i2MassChroQ because it implements a (peptide)identification-(protein)inference-mass-chromatogram-quantification processing workflow. The software benchmarking results reported in this paper show that i2MassChroQ performed better than competing software on two critical characteristics: (1) feature extraction capability and (2) protein quantitative dynamic range. Altogether, i2MassChroQ yielded better quantified protein numbers, both in a technical replicate MS runs setting and in a differential protein abundance analysis setting.
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Affiliation(s)
- Olivier Langella
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Thomas Renne
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Thierry Balliau
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Marlène Davanture
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Sven Brehmer
- Bruker Software Development, Bruker Daltonics GmbH & Co. KG, Bremen D-28359, Germany
| | - Michel Zivy
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Mélisande Blein-Nicolas
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Filippo Rusconi
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
- INSERM, UMR-S 1138, Centre de Recherche des Cordeliers, Paris F-75005, France
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5
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Baudouin L, Adès N, Kanté K, Bachelin C, Hmidan H, Deboux C, Panic R, Ben Messaoud R, Velut Y, Hamada S, Pionneau C, Duarte K, Poëa-Guyon S, Barnier JV, Nait Oumesmar B, Bouslama-Oueghlani L. Antagonistic actions of PAK1 and NF2/Merlin drive myelin membrane expansion in oligodendrocytes. Glia 2024; 72:1518-1540. [PMID: 38794866 DOI: 10.1002/glia.24570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
In the central nervous system, the formation of myelin by oligodendrocytes (OLs) relies on the switch from the polymerization of the actin cytoskeleton to its depolymerization. The molecular mechanisms that trigger this switch have yet to be elucidated. Here, we identified P21-activated kinase 1 (PAK1) as a major regulator of actin depolymerization in OLs. Our results demonstrate that PAK1 accumulates in OLs in a kinase-inhibited form, triggering actin disassembly and, consequently, myelin membrane expansion. Remarkably, proteomic analysis of PAK1 binding partners enabled the identification of NF2/Merlin as its endogenous inhibitor. Our findings indicate that Nf2 knockdown in OLs results in PAK1 activation, actin polymerization, and a reduction in OL myelin membrane expansion. This effect is rescued by treatment with a PAK1 inhibitor. We also provide evidence that the specific Pak1 loss-of-function in oligodendroglia stimulates the thickening of myelin sheaths in vivo. Overall, our data indicate that the antagonistic actions of PAK1 and NF2/Merlin on the actin cytoskeleton of the OLs are critical for proper myelin formation. These findings have broad mechanistic and therapeutic implications in demyelinating diseases and neurodevelopmental disorders.
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Affiliation(s)
- Lucas Baudouin
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Noémie Adès
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Kadia Kanté
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Corinne Bachelin
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Hatem Hmidan
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié-Salpêtrière, Paris, France
- Al-Quds University, Faculty of Medicine, Jerusalem, Palestine
| | - Cyrille Deboux
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Radmila Panic
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Rémy Ben Messaoud
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Yoan Velut
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Paris, France
| | - Soumia Hamada
- Sorbonne Université, Inserm, UMS Production et Analyse des Données en Sciences de la vie et en Santé, PASS, Plateforme Post-génomique de la Pitié-Salpêtrière, Paris, France
| | - Cédric Pionneau
- Sorbonne Université, Inserm, UMS Production et Analyse des Données en Sciences de la vie et en Santé, PASS, Plateforme Post-génomique de la Pitié-Salpêtrière, Paris, France
| | - Kévin Duarte
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - Sandrine Poëa-Guyon
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - Jean-Vianney Barnier
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - Brahim Nait Oumesmar
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Lamia Bouslama-Oueghlani
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié-Salpêtrière, Paris, France
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6
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Réthoré E, Pelletier S, Balliau T, Zivy M, Avelange-Macherel MH, Macherel D. Multi-scale analysis of heat stress acclimation in Arabidopsis seedlings highlights the primordial contribution of energy-transducing organelles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:300-331. [PMID: 38613336 DOI: 10.1111/tpj.16763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 04/14/2024]
Abstract
Much progress has been made in understanding the molecular mechanisms of plant adaptation to heat stress. However, the great diversity of models and stress conditions, and the fact that analyses are often limited to a small number of approaches, complicate the picture. We took advantage of a liquid culture system in which Arabidopsis seedlings are arrested in their development, thus avoiding interference with development and drought stress responses, to investigate through an integrative approach seedlings' global response to heat stress and acclimation. Seedlings perfectly tolerate a noxious heat shock (43°C) when subjected to a heat priming treatment at a lower temperature (38°C) the day before, displaying a thermotolerance comparable to that previously observed for Arabidopsis. A major effect of the pre-treatment was to partially protect energy metabolism under heat shock and favor its subsequent rapid recovery, which was correlated with the survival of seedlings. Rapid recovery of actin cytoskeleton and mitochondrial dynamics were another landmark of heat shock tolerance. The omics confirmed the role of the ubiquitous heat shock response actors but also revealed specific or overlapping responses to priming, heat shock, and their combination. Since only a few components or functions of chloroplast and mitochondria were highlighted in these analyses, the preservation and rapid recovery of their bioenergetic roles upon acute heat stress do not require extensive remodeling of the organelles. Protection of these organelles is rather integrated into the overall heat shock response, thus allowing them to provide the energy required to elaborate other cellular responses toward acclimation.
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Affiliation(s)
- Elise Réthoré
- Univ Angers, Institut Agro Rennes-Angers, INRAE, IRHS-UMR 1345, F-49000, Angers, France
| | - Sandra Pelletier
- Univ Angers, Institut Agro Rennes-Angers, INRAE, IRHS-UMR 1345, F-49000, Angers, France
| | - Thierry Balliau
- INRAE, PAPPSO, UMR/UMR Génétique Végétale, Gif sur Yvette, France
| | - Michel Zivy
- INRAE, PAPPSO, UMR/UMR Génétique Végétale, Gif sur Yvette, France
| | | | - David Macherel
- Univ Angers, Institut Agro Rennes-Angers, INRAE, IRHS-UMR 1345, F-49000, Angers, France
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Suárez SE, Rabesona H, Ménard O, Jardin J, Anton M, Cristina Añón M. Dynamic digestion of a high protein beverage based on amaranth: Structural changes and antihypertensive activity. Food Res Int 2024; 187:114416. [PMID: 38763666 DOI: 10.1016/j.foodres.2024.114416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/20/2024] [Accepted: 04/22/2024] [Indexed: 05/21/2024]
Abstract
An amaranth beverage (AB) was subjected to a simulated process of dynamic gastrointestinal digestion DIDGI®, a simple two-compartment in vitro dynamic gastrointestinal digestion system. The structural changes caused to the proteins during digestion and the digesta inhibitory capacity of the angiotensin converting enzyme (ACE) were investigated. In gastric compartment the degree of hydrolysis (DH) was 14.7 ± 1.5 % and in the intestinal compartment, proteins were digests in a greater extent (DH = 60.6 ± 8.4 %). Protein aggregation was detected during the gastric phase. The final digesta obtained both at the gastric and intestinal level, showed ACE inhibitory capacity (IC50 80 ± 10 and 140 ± 20 μg/mL, respectively). Purified fractions from these digesta showed even greater inhibitory capacity, being eluted 2 (E2) the most active fraction (IC50 60 ± 10 μg/mL). Twenty-six peptide sequences were identified. Six of them, with potential antihypertensive capacity, belong to A. hypochondriacus, 3 agglutinins and 3 encrypted sequences in the 11S globulin. Results obtained provide new and useful information on peptides released from the digestion of an amaranth based beverage and its ACE bioactivity.
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Affiliation(s)
- Santiago E Suárez
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos (CIDCA), Facultad de Ciencias Exactas, UNLP. CIC. CONICET (Consejo Nacional de Investigaciones Científica y Técnicas), Calle 47 y 116 - 1900, La Plata, Argentina; INRAE, UR BIA, F-44316 Nantes, France; INRAE, Institut AGRO, STLO, 35042 Rennes, France
| | | | | | | | | | - María Cristina Añón
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos (CIDCA), Facultad de Ciencias Exactas, UNLP. CIC. CONICET (Consejo Nacional de Investigaciones Científica y Técnicas), Calle 47 y 116 - 1900, La Plata, Argentina.
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8
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Bahammou D, Recorbet G, Mamode Cassim A, Robert F, Balliau T, Van Delft P, Haddad Y, Mongrand S, Fouillen L, Simon-Plas F. A combined lipidomic and proteomic profiling of Arabidopsis thaliana plasma membrane. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38761101 DOI: 10.1111/tpj.16810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 05/20/2024]
Abstract
The plant plasma membrane (PM) plays a key role in perception of environmental signals, and set-up of adaptive responses. An exhaustive and quantitative description of the whole set of lipids and proteins constituting the PM is necessary to understand how these components allow to fulfill such essential physiological functions. Here we provide by state-of-the-art approaches the first combined reference of the plant PM lipidome and proteome from Arabidopsis thaliana suspension cell culture. We identified and quantified a reproducible core set of 2165 proteins, which is by far the largest set of available data concerning this plant PM proteome. Using the same samples, combined lipidomic approaches, allowing the identification and quantification of an unprecedented repertoire of 414 molecular species of lipids showed that sterols, phospholipids, and sphingolipids are present in similar proportions in the plant PM. Within each lipid class, the precise amount of each lipid family and the relative proportion of each molecular species were further determined, allowing to establish the complete lipidome of Arabidopsis PM, and highlighting specific characteristics of the different molecular species of lipids. Results obtained point to a finely tuned adjustment of the molecular characteristics of lipids and proteins. More than a hundred proteins related to lipid metabolism, transport, or signaling have been identified and put in perspective of the lipids with which they are associated. This set of data represents an innovative resource to guide further research relative to the organization and functions of the plant PM.
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Affiliation(s)
- Delphine Bahammou
- Laboratoire de Biogenèse Membranaire, CNRS, Université, Bordeaux, (UMR 5200), F-33140, Villenave d'Ornon, France
| | - Ghislaine Recorbet
- UMR Agroécologie, INRAE, Institut Agro Dijon, Université Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Adiilah Mamode Cassim
- UMR Agroécologie, INRAE, Institut Agro Dijon, Université Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Franck Robert
- UMR Agroécologie, INRAE, Institut Agro Dijon, Université Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Thierry Balliau
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, PAPPSO, F-91190, Gif-Sur-Yvette, France
| | - Pierre Van Delft
- Laboratoire de Biogenèse Membranaire, CNRS, Université, Bordeaux, (UMR 5200), F-33140, Villenave d'Ornon, France
| | - Youcef Haddad
- Laboratoire de Biogenèse Membranaire, CNRS, Université, Bordeaux, (UMR 5200), F-33140, Villenave d'Ornon, France
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire, CNRS, Université, Bordeaux, (UMR 5200), F-33140, Villenave d'Ornon, France
| | - Laetitia Fouillen
- Laboratoire de Biogenèse Membranaire, CNRS, Université, Bordeaux, (UMR 5200), F-33140, Villenave d'Ornon, France
| | - Françoise Simon-Plas
- UMR Agroécologie, INRAE, Institut Agro Dijon, Université Bourgogne Franche-Comté, F-21000, Dijon, France
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9
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Berkel Kasikci M, Guilois-Dubois S, Billet K, Jardin J, Guyot S, Morzel M. Interactions between Salivary Proteins and Apple Polyphenols and the Fate of Complexes during Gastric Digestion. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38603459 DOI: 10.1021/acs.jafc.4c00468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Beneficial polyphenols in apples can reach the stomach as complexes formed with salivary proteins. The present study aimed at documenting the interactions between salivary proteins and cider apple polyphenols and the fate of complexes during gastric digestion. A polyphenolic extract was mixed with human saliva, and interactions were characterized by analyzing proteins and polyphenols in the insoluble and soluble fractions of the mixtures, before and after in vitro gastric digestion. Results confirmed that proline-rich proteins can efficiently precipitate polyphenols and suggested that two zinc-binding proteins can also form insoluble complexes with polyphenols. The classes of polyphenols involved in such complexes depended on the polyphenol-to-protein ratio. In vitro gastric digestion led to extensive proteolysis of salivary proteins, and we formulate the hypothesis that the resulting peptides can interact with and precipitate some procyanidins. Saliva may therefore partly modulate the bioaccessibility of at least procyanidins in the gastric compartment.
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Affiliation(s)
- Müzeyyen Berkel Kasikci
- INRAE, Institut Agro, STLO, 35042 Rennes, France
- Department of Food Engineering, Manisa Celal Bayar University, 45140 Manisa, Turkey
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10
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Voedts H, Anoyatis-Pelé C, Langella O, Rusconi F, Hugonnet JE, Arthur M. (p)ppGpp modifies RNAP function to confer β-lactam resistance in a peptidoglycan-independent manner. Nat Microbiol 2024; 9:647-656. [PMID: 38443580 DOI: 10.1038/s41564-024-01609-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 01/16/2024] [Indexed: 03/07/2024]
Abstract
(p)ppGpp is a nucleotide alarmone that controls bacterial response to nutrient deprivation. Since elevated (p)ppGpp levels confer mecillinam resistance and are essential for broad-spectrum β-lactam resistance as mediated by the β-lactam-insensitive transpeptidase YcbB (LdtD), we hypothesized that (p)ppGpp might affect cell wall peptidoglycan metabolism. Here we report that (p)ppGpp-dependent β-lactam resistance does not rely on any modification of peptidoglycan metabolism, as established by analysis of Escherichia coli peptidoglycan structure using high-resolution mass spectrometry. Amino acid substitutions in the β or β' RNA polymerase (RNAP) subunits, alone or in combination with the CRISPR interference-mediated downregulation of three of seven ribosomal RNA operons, were sufficient for resistance, although β-lactams have no known impact on the RNAP or ribosomes. This implies that modifications of RNAP and ribosome functions are critical to prevent downstream effects of the inactivation of peptidoglycan transpeptidases by β-lactams.
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Affiliation(s)
- Henri Voedts
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
| | - Constantin Anoyatis-Pelé
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
| | - Olivier Langella
- GQE-Le Moulon/PAPPSO, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, Gif-sur-Yvette, France
| | - Filippo Rusconi
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
- GQE-Le Moulon/PAPPSO, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, Gif-sur-Yvette, France
| | - Jean-Emmanuel Hugonnet
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France.
| | - Michel Arthur
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France.
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11
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Delogu F, Kunath BJ, Queirós PM, Halder R, Lebrun LA, Pope PB, May P, Widder S, Muller EEL, Wilmes P. Forecasting the dynamics of a complex microbial community using integrated meta-omics. Nat Ecol Evol 2024; 8:32-44. [PMID: 37957315 PMCID: PMC10781640 DOI: 10.1038/s41559-023-02241-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 10/02/2023] [Indexed: 11/15/2023]
Abstract
Predicting the behaviour of complex microbial communities is challenging. However, this is essential for complex biotechnological processes such as those in biological wastewater treatment plants (BWWTPs), which require sustainable operation. Here we summarize 14 months of longitudinal meta-omics data from a BWWTP anaerobic tank into 17 temporal signals, explaining 91.1% of the temporal variance, and link those signals to ecological events within the community. We forecast the signals over the subsequent five years and use 21 extra samples collected at defined time intervals for testing and validation. Our forecasts are correct for six signals and hint on phenomena such as predation cycles. Using all the 17 forecasts and the environmental variables, we predict gene abundance and expression, with a coefficient of determination ≥0.87 for the subsequent three years. Our study demonstrates the ability to forecast the dynamics of open microbial ecosystems using interactions between community cycles and environmental parameters.
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Affiliation(s)
- Francesco Delogu
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - Benoit J Kunath
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Pedro M Queirós
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laura A Lebrun
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Phillip B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Stefanie Widder
- Department of Medicine 1, Research Division Infection Biology, Medical University of Vienna, Vienna, Austria
| | - Emilie E L Muller
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156 CNRS, Université de Strasbourg, Strasbourg, France
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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12
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Tarkowski ŁP, Clochard T, Blein-Nicolas M, Zivy M, Baillau T, Abadie C, Morère-Le Paven MC, Limami AM, Tcherkez G, Montrichard F. The nitrate transporter-sensor MtNPF6.8 regulates the branched chain amino acid/pantothenate metabolic pathway in barrel medic (Medicago truncatula Gaertn.) root tip. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108213. [PMID: 38043253 DOI: 10.1016/j.plaphy.2023.108213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/02/2023] [Accepted: 11/19/2023] [Indexed: 12/05/2023]
Abstract
Nitrogen is the most limiting nutrient for plants, and it is preferentially absorbed in the form of nitrate by roots, which adapt to nitrate fluctuations by remodelling their architecture. Although core mechanisms of the response to nitrate availability are relatively well-known, signalling events controlling root growth and architecture have not all been identified, in particular in Legumes. However, the developmental effect of nitrate in Legumes is critical since external nitrate not only regulates root architecture but also N2-fixing nodule development. We have previously shown that in barrel medic (Medicago truncatula), the nitrate transporter MtNPF6.8 is required for nitrate sensitivity in root tip. However, uncertainty remains as to whether nitrogen metabolism itself is involved in the MtNPF6.8-mediated response. Here, we examine the metabolic effects of MtNPF6.8-dependent nitrate signalling using metabolomics and proteomics in WT and mtnpf6.8 root tips in presence or absence of nitrate. We found a reorchestration of metabolism due to the mutation, in favour of the branched chain amino acids/pantothenate metabolic pathway, and lipid catabolism via glyoxylate. That is, the mtnpf6.8 mutation was likely associated with a specific rerouting of acetyl-CoA production (glyoxylic cycle) and utilisation (pantothenate and branched chain amino acid synthesis). In agreement with our previous findings, class III peroxidases were confirmed as the main protein class responsive to nitrate, although in an MtNPF6.8-independent fashion. Our data rather suggest the involvement of other pathways within mtnpf6.8 root tips, such as Ca2+ signalling or cell wall methylation.
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Affiliation(s)
| | | | - Mélisande Blein-Nicolas
- GQE - Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Gif-sur-Yvette, France
| | - Michel Zivy
- GQE - Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Gif-sur-Yvette, France
| | - Thierry Baillau
- GQE - Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Gif-sur-Yvette, France
| | - Cyril Abadie
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | | | - Anis M Limami
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Guillaume Tcherkez
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France; Research School of Biology, ANU Joint College of Sciences, Australian National University, Canberra, Australia
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13
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Ngom SI, Maski S, Rached B, Chouati T, Oliveira Correia L, Juste C, Meylheuc T, Henrissat B, El Fahime E, Amar M, Béra-Maillet C. Exploring the hemicellulolytic properties and safety of Bacillus paralicheniformis as stepping stone in the use of new fibrolytic beneficial microbes. Sci Rep 2023; 13:22785. [PMID: 38129471 PMCID: PMC10740013 DOI: 10.1038/s41598-023-49724-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Bacillus strains from the Moroccan Coordinated Collections of Microorganisms (CCMM) were characterised and tested for fibrolytic function and safety properties that would be beneficial for maintaining intestinal homeostasis, and recommend beneficial microbes in the field of health promotion research. Forty strains were investigated for their fibrolytic activities towards complex purified polysaccharides and natural fibres representative of dietary fibres (DFs) entering the colon for digestion. We demonstrated hemicellulolytic activities for nine strains of Bacillus aerius, re-identified as Bacillus paralicheniformis and Bacillus licheniformis, using xylan, xyloglucan or lichenan as purified polysaccharides, and orange, apple and carrot natural fibres, with strain- and substrate-dependent production of glycoside hydrolases (GHs). Our combined methods, based on enzymatic assays, secretome, and genome analyses, highlighted the hemicellulolytic activities of B. paralicheniformis and the secretion of specific glycoside hydrolases, in particular xylanases, compared to B. licheniformis. Genomic features of these strains revealed a complete set of GH genes dedicated to the degradation of various polysaccharides from DFs, including cellulose, hemicellulose and pectin, which may confer on the strains the ability to digest a variety of DFs. Preliminary experiments on the safety and immunomodulatory properties of B. paralicheniformis fibrolytic strains were evaluated in light of applications as beneficial microbes' candidates for health improvement. B. paralicheniformis CCMM B969 was therefore proposed as a new fibrolytic beneficial microbe candidate.
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Affiliation(s)
- Serigne Inssa Ngom
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Soufiane Maski
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Département de Biologie, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
| | - Bahia Rached
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Laboratoire de Chimie-Physique et Biotechnologies des Biomolécules et Matériaux/Equipe Microbiologie Biomolécules et Biotechnologies, Faculté des Sciences et Techniques, Mohammedia, Morocco
| | - Taha Chouati
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Biologie médicale, Pathologie humaine et Expérimentale et Environnement, Faculté de Médecine et de pharmacie de Rabat, Rabat, Morocco
| | - Lydie Oliveira Correia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, PAPPSO, 78350, Jouy-en-Josas, France
| | - Catherine Juste
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Thierry Meylheuc
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, MIMA2, 78350, Jouy en Josas, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, 13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Elmostafa El Fahime
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Biologie médicale, Pathologie humaine et Expérimentale et Environnement, Faculté de Médecine et de pharmacie de Rabat, Rabat, Morocco
| | - Mohamed Amar
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
| | - Christel Béra-Maillet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco.
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14
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da Silva TF, Glória RDA, de Sousa TJ, Americo MF, Freitas ADS, Viana MVC, de Jesus LCL, da Silva Prado LC, Daniel N, Ménard O, Cochet MF, Dupont D, Jardin J, Borges AD, Fernandes SOA, Cardoso VN, Brenig B, Ferreira E, Profeta R, Aburjaile FF, de Carvalho RDO, Langella P, Le Loir Y, Cherbuy C, Jan G, Azevedo V, Guédon É. Comprehensive probiogenomics analysis of the commensal Escherichia coli CEC15 as a potential probiotic strain. BMC Microbiol 2023; 23:364. [PMID: 38008714 PMCID: PMC10680302 DOI: 10.1186/s12866-023-03112-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/06/2023] [Indexed: 11/28/2023] Open
Abstract
BACKGROUND Probiotics have gained attention for their potential maintaining gut and immune homeostasis. They have been found to confer protection against pathogen colonization, possess immunomodulatory effects, enhance gut barrier functionality, and mitigate inflammation. However, a thorough understanding of the unique mechanisms of effects triggered by individual strains is necessary to optimize their therapeutic efficacy. Probiogenomics, involving high-throughput techniques, can help identify uncharacterized strains and aid in the rational selection of new probiotics. This study evaluates the potential of the Escherichia coli CEC15 strain as a probiotic through in silico, in vitro, and in vivo analyses, comparing it to the well-known probiotic reference E. coli Nissle 1917. Genomic analysis was conducted to identify traits with potential beneficial activity and to assess the safety of each strain (genomic islands, bacteriocin production, antibiotic resistance, production of proteins involved in host homeostasis, and proteins with adhesive properties). In vitro studies assessed survival in gastrointestinal simulated conditions and adhesion to cultured human intestinal cells. Safety was evaluated in BALB/c mice, monitoring the impact of E. coli consumption on clinical signs, intestinal architecture, intestinal permeability, and fecal microbiota. Additionally, the protective effects of both strains were assessed in a murine model of 5-FU-induced mucositis. RESULTS CEC15 mitigates inflammation, reinforces intestinal barrier, and modulates intestinal microbiota. In silico analysis revealed fewer pathogenicity-related traits in CEC15, when compared to Nissle 1917, with fewer toxin-associated genes and no gene suggesting the production of colibactin (a genotoxic agent). Most predicted antibiotic-resistance genes were neither associated with actual resistance, nor with transposable elements. The genome of CEC15 strain encodes proteins related to stress tolerance and to adhesion, in line with its better survival during digestion and higher adhesion to intestinal cells, when compared to Nissle 1917. Moreover, CEC15 exhibited beneficial effects on mice and their intestinal microbiota, both in healthy animals and against 5FU-induced intestinal mucositis. CONCLUSIONS These findings suggest that the CEC15 strain holds promise as a probiotic, as it could modulate the intestinal microbiota, providing immunomodulatory and anti-inflammatory effects, and reinforcing the intestinal barrier. These findings may have implications for the treatment of gastrointestinal disorders, particularly some forms of diarrhea.
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Affiliation(s)
- Tales Fernando da Silva
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Rafael de Assis Glória
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Thiago Jesus de Sousa
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Monique Ferrary Americo
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Andria Dos Santos Freitas
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Marcus Vinicius Canário Viana
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Luís Cláudio Lima de Jesus
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Nathalie Daniel
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Olivia Ménard
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Marie-Françoise Cochet
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Didier Dupont
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Julien Jardin
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Amanda Dias Borges
- Department of clinical and toxicological analysis, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Simone Odília Antunes Fernandes
- Department of clinical and toxicological analysis, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Valbert Nascimento Cardoso
- Department of clinical and toxicological analysis, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Bertram Brenig
- Department of Molecular Biology of Livestock, Institute of Veterinary Medicine, Georg-August Universität Göttingen, Göttingen, Germany
| | - Enio Ferreira
- Department of general pathology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Profeta
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Flavia Figueira Aburjaile
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Veterinary school, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Philippe Langella
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Yves Le Loir
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Claire Cherbuy
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Gwénaël Jan
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Vasco Azevedo
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Éric Guédon
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France.
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15
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Stander EA, Lehka B, Carqueijeiro I, Cuello C, Hansson FG, Jansen HJ, Dugé De Bernonville T, Birer Williams C, Vergès V, Lezin E, Lorensen MDBB, Dang TT, Oudin A, Lanoue A, Durand M, Giglioli-Guivarc'h N, Janfelt C, Papon N, Dirks RP, O'connor SE, Jensen MK, Besseau S, Courdavault V. The Rauvolfia tetraphylla genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids. Commun Biol 2023; 6:1197. [PMID: 38001233 PMCID: PMC10673892 DOI: 10.1038/s42003-023-05574-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Monoterpene indole alkaloids (MIAs) are a structurally diverse family of specialized metabolites mainly produced in Gentianales to cope with environmental challenges. Due to their pharmacological properties, the biosynthetic modalities of several MIA types have been elucidated but not that of the yohimbanes. Here, we combine metabolomics, proteomics, transcriptomics and genome sequencing of Rauvolfia tetraphylla with machine learning to discover the unexpected multiple actors of this natural product synthesis. We identify a medium chain dehydrogenase/reductase (MDR) that produces a mixture of four diastereomers of yohimbanes including the well-known yohimbine and rauwolscine. In addition to this multifunctional yohimbane synthase (YOS), an MDR synthesizing mainly heteroyohimbanes and the short chain dehydrogenase vitrosamine synthase also display a yohimbane synthase side activity. Lastly, we establish that the combination of geissoschizine synthase with at least three other MDRs also produces a yohimbane mixture thus shedding light on the complex mechanisms evolved for the synthesis of these plant bioactives.
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Affiliation(s)
- Emily Amor Stander
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Beata Lehka
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Inês Carqueijeiro
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Clément Cuello
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Frederik G Hansson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Hans J Jansen
- Future Genomics Technologies, 2333 BE, Leiden, The Netherlands
| | - Thomas Dugé De Bernonville
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
- Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Caroline Birer Williams
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Valentin Vergès
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Enzo Lezin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | | | - Thu-Thuy Dang
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada
| | - Audrey Oudin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Arnaud Lanoue
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Mickael Durand
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | | | - Christian Janfelt
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000, Angers, France
| | - Ron P Dirks
- Future Genomics Technologies, 2333 BE, Leiden, The Netherlands
| | - Sarah Ellen O'connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany.
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark.
| | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France.
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France.
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16
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Lavoisier A, Morzel M, Chevalier S, Henry G, Jardin J, Harel-Oger M, Garric G, Dupont D. In vitro digestion of two protein-rich dairy products in the ageing gastrointestinal tract. Food Funct 2023; 14:9377-9390. [PMID: 37789767 DOI: 10.1039/d3fo02693k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
It is still unclear if changes in protein digestibility and absorption kinetics in old age may affect the anabolic effect of high-protein foods. The objective of this study was to investigate the digestion of two high-protein (10% w/w) dairy products in vitro: a fermented dairy product formulated with a ratio of whey proteins to caseins of 80 to 20% (WBD) and a Skyr containing mainly caseins. The new static in vitro digestion model adapted to the general older adult population (≥65 years) proposed by the INFOGEST international consortium was implemented to investigate the digestion of these products and compared with the standard version of the protocol. Kinetics of proteolysis was compared between both models for each product, in the gastric and intestinal phases of digestion. Protein hydrolysis was studied by the OPA method, SDS-PAGE, and LC-MS/MS, and amino acids were quantified by HPLC. Protein hydrolysis by pepsin was slower with the older adult model than with the young adult model, and consequently, in spite of a longer gastric phase duration, the degree of proteolysis (DH) at the end of the gastric phase was lower. Two different scenarios were observed depending on the type of dairy product studied: -10 and -40% DH for Skyr and WBD, respectively. In the intestinal phase, lower concentrations of free leucine were observed in older adult conditions (approx. -10%), but no significant differences in proteolysis were observed overall between the models. Therefore, the digestion conditions used influenced significantly the rate and extent of proteolysis in the gastric phase but not in the intestinal phase.
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17
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Le Guillou S, Ciobotaru C, Laubier J, Castille J, Aujean E, Hue-Beauvais C, Cherbuy C, Liuu S, Henry C, David A, Jaffrezic F, Laloë D, Charlier M, Alexandre-Gouabau MC, Le Provost F. Specific Milk Composition of miR-30b Transgenic Mice Associated with Early Duodenum Maturation in Offspring with Lasting Consequences for Growth. J Nutr 2023; 153:2808-2826. [PMID: 37543213 DOI: 10.1016/j.tjnut.2023.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/18/2023] [Accepted: 08/01/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND Milk composition is complex and includes numerous components essential for offspring growth and development. In addition to the high abundance of miR-30b microRNA, milk produced by the transgenic mouse model of miR-30b-mammary deregulation displays a significantly altered fatty acid profile. Moreover, wild-type adopted pups fed miR-30b milk present an early growth defect. OBJECTIVE This study aimed to investigate the consequences of miR-30b milk feeding on the duodenal development of wild-type neonates, a prime target of suckled milk, along with comprehensive milk phenotyping. METHODS The duodenums of wild-type pups fed miR-30b milk were extensively characterized at postnatal day (PND)-5, PND-6, and PND-15 using histological, transcriptomic, proteomic, and duodenal permeability analyses and compared with those of pups fed wild-type milk. Milk of miR-30b foster dams collected at mid-lactation was extensively analyzed using proteomic, metabolomic, and lipidomic approaches and hormonal immunoassays. RESULTS At PND-5, wild-type pups fed miR-30b milk showed maturation of their duodenum with 1.5-fold (P < 0.05) and 1.3-fold (P < 0.10) increased expression of Claudin-3 and Claudin-4, respectively, and changes in 8 duodenal proteins (P < 0.10), with an earlier reduction in paracellular and transcellular permeability (183 ng/mL fluorescein sulfonic acid [FSA] and 12 ng/mL horseradish peroxidase [HRP], respectively, compared with 5700 ng/mL FSA and 90 ng/mL HRP in wild-type; P < 0.001). Compared with wild-type milk, miR-30b milk displayed an increase in total lipid (219 g/L compared with 151 g/L; P < 0.05), ceramide (17.6 μM compared with 6.9 μM; P < 0.05), and sphingomyelin concentrations (163.7 μM compared with 76.3 μM; P < 0.05); overexpression of 9 proteins involved in the gut barrier (P < 0.1); and higher insulin and leptin concentrations (1.88 ng/mL and 2.04 ng/mL, respectively, compared with 0.79 ng/mL and 1.06 ng/mL; P < 0.01). CONCLUSIONS miR-30b milk displays significant changes in bioactive components associated with neonatal duodenal integrity and maturation, which could be involved in the earlier intestinal closure phenotype of the wild-type pups associated with a lower growth rate.
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Affiliation(s)
| | - Céline Ciobotaru
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Johann Laubier
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Johan Castille
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Etienne Aujean
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Cathy Hue-Beauvais
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Claire Cherbuy
- Université Paris-Saclay, INRAE, MICALIS Institute, Jouy-en-Josas, France
| | - Sophie Liuu
- Université Paris-Saclay, INRAE, AgroParisTech, MICALIS Institute, PAPPSO, Jouy-en-Josas, France
| | - Céline Henry
- Université Paris-Saclay, INRAE, AgroParisTech, MICALIS Institute, PAPPSO, Jouy-en-Josas, France
| | - Agnès David
- Nantes Université, CRNH-OUEST, INRAE, UMR 1280, PhAN, Nantes, France
| | - Florence Jaffrezic
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Denis Laloë
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Madia Charlier
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
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18
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Zhang B, Lingga C, De Groot H, Hackmann TJ. The oxidoreductase activity of Rnf balances redox cofactors during fermentation of glucose to propionate in Prevotella. Sci Rep 2023; 13:16429. [PMID: 37777597 PMCID: PMC10542786 DOI: 10.1038/s41598-023-43282-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/21/2023] [Indexed: 10/02/2023] Open
Abstract
Propionate is a microbial metabolite formed in the gastrointestinal tract, and it affects host physiology as a source of energy and signaling molecule. Despite the importance of propionate, the biochemical pathways responsible for its formation are not clear in all microbes. For the succinate pathway used during fermentation, a key enzyme appears to be missing-one that oxidizes ferredoxin and reduces NAD. Here we show that Rnf [ferredoxin-NAD+ oxidoreductase (Na+-transporting)] is this key enzyme in two abundant bacteria of the rumen (Prevotella brevis and Prevotella ruminicola). We found these bacteria form propionate, succinate, and acetate with the classic succinate pathway. Without ferredoxin:NAD+ oxidoreductase, redox cofactors would be unbalanced; it would produce almost equal excess amounts of reduced ferredoxin and oxidized NAD. By combining growth experiments, genomics, proteomics, and enzyme assays, we point to the possibility that these bacteria solve this problem by oxidizing ferredoxin and reducing NAD with Rnf [ferredoxin-NAD+ oxidoreductase (Na+-transporting)]. Genomic and phenotypic data suggest many bacteria may use Rnf similarly. This work shows the ferredoxin:NAD+ oxidoreductase activity of Rnf is important to propionate formation in Prevotella species and other bacteria from the environment, and it provides fundamental knowledge for manipulating fermentative propionate production.
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Affiliation(s)
- Bo Zhang
- Department of Animal Science, University of California, Davis, CA, USA
| | | | - Hannah De Groot
- Department of Animal Science, University of California, Davis, CA, USA
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19
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Duruflé H, Balliau T, Blanchet N, Chaubet A, Duhnen A, Pouilly N, Blein-Nicolas M, Mangin B, Maury P, Langlade NB, Zivy M. Sunflower Hybrids and Inbred Lines Adopt Different Physiological Strategies and Proteome Responses to Cope with Water Deficit. Biomolecules 2023; 13:1110. [PMID: 37509146 PMCID: PMC10377273 DOI: 10.3390/biom13071110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Sunflower is a hybrid crop that is considered moderately drought-tolerant and adapted to new cropping systems required for the agro-ecological transition. Here, we studied the impact of hybridity status (hybrids vs. inbred lines) on the responses to drought at the molecular and eco-physiological level exploiting publicly available datasets. Eco-physiological traits and leaf proteomes were measured in eight inbred lines and their sixteen hybrids grown in the high-throughput phenotyping platform Phenotoul-Heliaphen. Hybrids and parental lines showed different growth strategies: hybrids grew faster in the absence of water constraint and arrested their growth more abruptly than inbred lines when subjected to water deficit. We identified 471 differentially accumulated proteins, of which 256 were regulated by drought. The amplitude of up- and downregulations was greater in hybrids than in inbred lines. Our results show that hybrids respond more strongly to water deficit at the molecular and eco-physiological levels. Because of presence/absence polymorphism, hybrids potentially contain more genes than their parental inbred lines. We propose that detrimental homozygous mutations and the lower number of genes in inbred lines lead to a constitutive defense mechanism that may explain the lower growth of inbred lines under well-watered conditions and their lower reactivity to water deficit.
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Affiliation(s)
- Harold Duruflé
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
- INRAE, ONF, BioForA, 45075 Orleans, France
| | - Thierry Balliau
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
| | - Nicolas Blanchet
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Adeline Chaubet
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Alexandra Duhnen
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Nicolas Pouilly
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Mélisande Blein-Nicolas
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
| | - Brigitte Mangin
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Pierre Maury
- INRAE, INP-ENSAT Toulouse, UMR AGIR, Université de Toulouse, 31000 Toulouse, France
| | | | - Michel Zivy
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
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20
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Chauvet L, Ménard O, Le Gouar Y, Henry G, Jardin J, Hennetier M, Croguennec T, Van Audenhaege M, Dupont D, Lemaire M, Le Huërou-Luron I, Deglaire A. Protein ingredient quality of infant formulas impacts their structure and kinetics of proteolysis under in vitro dynamic digestion. Food Res Int 2023; 169:112883. [PMID: 37254331 DOI: 10.1016/j.foodres.2023.112883] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 06/01/2023]
Abstract
Infant formula (IF) is a complex matrix requiring numerous ingredients and processing steps. The objective was to understand how the quality of protein ingredients impacts IF structure and, in turn, their kinetics of digestion. Four powdered IFs (A/B/C/D), based on commercial whey protein (WP) ingredients, with different protein denaturation levels and composition (A/B/C), and on caseins with different supramolecular organisations (C/D), were produced at a semi-industrial level after homogenization and spray-drying. Once reconstituted in water (13 %, wt/wt), the IF microstructure was analysed with asymmetrical flow field-flow fractionation coupled with multi-angle light scattering and differential refractometer, transmission electron microscopy and electrophoresis. The rehydrated IFs were subjected to simulated infant in vitro dynamic digestion (DIDGI®). Digesta were regularly sampled to follow structural changes (confocal microscopy, laser-light scattering) and proteolysis (OPA, SDS-PAGE, LC-MS/MS, cation-exchange chromatography). Before digestion, different microstructures were observed among IFs. IF-A, characterized by more denatured WPs, presented star-shaped mixed aggregates, with protein aggregates bounded to casein micelles, themselves adsorbed at the fat droplet interface. Non-micellar caseins, brought by non-micellar casein powder (IF-D) underwent rearrangement and aggregation at the interface of flocculated fat droplets, leading to a largely different microstructure of IF emulsion, with large aggregates of lipids and proteins. During digestion, IF-A more digested (degree of proteolysis + 16 %) at 180 min of intestinal phase than IF-C/D. The modification of the supramolecular organisation of caseins implied different kinetics of peptide release derived from caseins during the gastric phase (more abundant at G80 for IF-D). Bioactive peptide release kinetics were also different during digestion with IF-C presenting a maximal abundance for a large proportion of them. Overall, the present study highlights the importance of the structure and composition of the protein ingredients (WPs and caseins) selected for IF formulation on the final IF structure and, in turn, on proteolysis. Whether it has some physiological consequences remains to be investigated.
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Affiliation(s)
- Lucile Chauvet
- INRAE, Institut Agro, STLO, 35042 Rennes, France; Institut NuMeCan, INRAE, INSERM, Univ Rennes, Saint Gilles, France; SODIAAL International, Centre Recherche & Innovation, Rennes, France
| | | | | | | | | | - Marie Hennetier
- Université de Toulouse, Institut National Polytechnique de Toulouse - Ecole d'ingénieur de Purpan, Département Sciences Agronomique et Agroalimentaire, Toulouse, France
| | | | | | | | - Marion Lemaire
- SODIAAL International, Centre Recherche & Innovation, Rennes, France
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21
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Galio L, Bernet L, Rodriguez Y, Fourcault C, Dieudonné M, Pinatel H, Henry C, Sérazin V, Fathallah K, Gagneux A, Krupova Z, Vialard F, Santos ED. The effect of obesity on uterine receptivity is mediated by endometrial extracellular vesicles that control human endometrial stromal cell decidualization and trophoblast invasion. JOURNAL OF EXTRACELLULAR BIOLOGY 2023; 2:e103. [PMID: 38939074 PMCID: PMC11080792 DOI: 10.1002/jex2.103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/30/2023] [Accepted: 07/08/2023] [Indexed: 06/29/2024]
Abstract
The objectives of the present study were to determine whether obesity impacts human decidualization and the endometrial control of trophoblast invasion (both of which are required for embryo implantation) and evaluate the potential involvement of endometrial extracellular vesicles (EVs) in the regulation of these physiological processes. Using primary human cell cultures, we first demonstrated that obesity is associated with significantly lower in vitro decidualization of endometrial stromal cells (ESCs). We then showed that a trophoblastic cell line's invasive ability was greater in the presence of conditioned media from cultures of ESCs from obese women. The results of functional assays indicated that supplementation of the culture medium with EVs from nonobese women can rescue (at least in part) the defect in in vitro decidualization described in ESCs from obese women. Furthermore, exposure to endometrial EVs from obese women (vs. nonobese women) was associated with significantly greater invasive activity by HTR-8/SVneo cells. Using mass-spectrometry-based quantitative proteomics, we found that EVs isolated from uterine supernatants of biopsies from obese women (vs. nonobese women) presented a molecular signature focused on cell remodelling and angiogenesis. The proteomics analysis revealed two differentially expressed proteins (fibronectin and angiotensin-converting enzyme) that might be involved specifically in the rescue of the decidualization capacity in ESCs from obese women; both of these proteins are abundantly present in endometrial EVs from nonobese women, and both are involved in the decidualization process. In conclusion, our results provided new insights into the endometrial EVs' pivotal role in the poor uterine receptivity observed in obese women.
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Affiliation(s)
- Laurent Galio
- Université Paris‐Saclay, UVSQ, INRAE, BREEDJouy‐en‐JosasFrance
- Ecole Nationale Vétérinaire d'Alfort, BREEDMaisons‐AlfortFrance
| | - Laetitia Bernet
- Université Paris‐Saclay, UVSQ, INRAE, BREEDJouy‐en‐JosasFrance
- Ecole Nationale Vétérinaire d'Alfort, BREEDMaisons‐AlfortFrance
| | - Yoann Rodriguez
- Université Paris‐Saclay, UVSQ, INRAE, BREEDJouy‐en‐JosasFrance
- Ecole Nationale Vétérinaire d'Alfort, BREEDMaisons‐AlfortFrance
| | - Camille Fourcault
- Université Paris‐Saclay, UVSQ, INRAE, BREEDJouy‐en‐JosasFrance
- Ecole Nationale Vétérinaire d'Alfort, BREEDMaisons‐AlfortFrance
| | - Marie‐Noëlle Dieudonné
- Université Paris‐Saclay, UVSQ, INRAE, BREEDJouy‐en‐JosasFrance
- Ecole Nationale Vétérinaire d'Alfort, BREEDMaisons‐AlfortFrance
| | - Hélène Pinatel
- Université Paris‐Saclay, UVSQ, INRAE, BREEDJouy‐en‐JosasFrance
- Ecole Nationale Vétérinaire d'Alfort, BREEDMaisons‐AlfortFrance
| | - Céline Henry
- Université Paris‐Saclay, INRAEAgroParisTech, Micalis Institute, PAPPSOJouy‐en‐JosasFrance
| | - Valérie Sérazin
- Université Paris‐Saclay, UVSQ, INRAE, BREEDJouy‐en‐JosasFrance
- Ecole Nationale Vétérinaire d'Alfort, BREEDMaisons‐AlfortFrance
- Service de Biologie MédicaleCentre Hospitalier de Poissy‐Saint GermainPoissyFrance
| | - Khadija Fathallah
- Service de Gynécologie et ObstétriqueCentre Hospitalier de Poissy‐Saint GermainPoissyFrance
| | - Anissa Gagneux
- Université Paris‐Saclay, UVSQ, INRAE, BREEDJouy‐en‐JosasFrance
- Ecole Nationale Vétérinaire d'Alfort, BREEDMaisons‐AlfortFrance
| | | | - François Vialard
- Université Paris‐Saclay, UVSQ, INRAE, BREEDJouy‐en‐JosasFrance
- Ecole Nationale Vétérinaire d'Alfort, BREEDMaisons‐AlfortFrance
- Service de Biologie MédicaleCentre Hospitalier de Poissy‐Saint GermainPoissyFrance
| | - Esther Dos Santos
- Université Paris‐Saclay, UVSQ, INRAE, BREEDJouy‐en‐JosasFrance
- Ecole Nationale Vétérinaire d'Alfort, BREEDMaisons‐AlfortFrance
- Service de Biologie MédicaleCentre Hospitalier de Poissy‐Saint GermainPoissyFrance
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22
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Rodovalho VDR, da Luz BSR, Nicolas A, Jardin J, Briard-Bion V, Folador EL, Santos AR, Jan G, Loir YL, Azevedo VADC, Guédon É. Different culture media and purification methods unveil the core proteome of Propionibacterium freudenreichii-derived extracellular vesicles. MICROLIFE 2023; 4:uqad029. [PMID: 37324655 PMCID: PMC10265600 DOI: 10.1093/femsml/uqad029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/12/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023]
Abstract
Bacterial extracellular vesicles (EVs) are natural lipidic nanoparticles implicated in intercellular communication. Although EV research focused mainly on pathogens, the interest in probiotic-derived EVs is now rising. One example is Propionibacterium freudenreichii, which produces EVs with anti-inflammatory effects on human epithelial cells. Our previous study with P. freudenreichii showed that EVs purified by size exclusion chromatography (SEC) displayed variations in protein content according to bacterial growth conditions. Considering these content variations, we hypothesized that a comparative proteomic analysis of EVs recovered in different conditions would elucidate whether a representative vesicular proteome existed, possibly providing a robust proteome dataset for further analysis. Therefore, P. freudenreichii was grown in two culture media, and EVs were purified by sucrose density gradient ultracentrifugation (UC). Microscopic and size characterization confirmed EV purification, while shotgun proteomics unveiled that they carried a diverse set of proteins. A comparative analysis of the protein content of UC- and SEC-derived EVs, isolated from cultures either in UF (cow milk ultrafiltrate medium) or YEL (laboratory yeast extract lactate medium), showed that EVs from all these conditions shared 308 proteins. This EV core proteome was notably enriched in proteins related to immunomodulation. Moreover, it showed distinctive features, including highly interacting proteins, compositional biases for some specific amino acids, and other biochemical parameters. Overall, this work broadens the toolset for the purification of P. freudenreichii-derived EVs, identifies a representative vesicular proteome, and enumerates conserved features in vesicular proteins. These results hold the potential for providing candidate biomarkers of purification quality, and insights into the mechanisms of EV biogenesis and cargo sorting.
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Affiliation(s)
- Vinícius de Rezende Rodovalho
- INRAE, Institut Agro, STLO, 35042, Rennes, France
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
- Laboratory of Immunoinflammation, Institute of Biology, University of Campinas (UNICAMP), Campinas 13000-000, Brazil
| | - Brenda Silva Rosa da Luz
- INRAE, Institut Agro, STLO, 35042, Rennes, France
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | | | | | | | - Edson Luiz Folador
- Center of Biotechnology, Department of Biotechnology, Federal University of Paraíba, João Pessoa 58051-900, Brazil
| | - Anderson Rodrigues Santos
- Faculty of Computer Science, Department of Computer Science, Federal University of Uberlândia, Uberlândia 38400902, Brazil
| | - Gwénaël Jan
- INRAE, Institut Agro, STLO, 35042, Rennes, France
| | - Yves Le Loir
- INRAE, Institut Agro, STLO, 35042, Rennes, France
| | - Vasco Ariston de Carvalho Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Éric Guédon
- Corresponding author. INRAE, Institut Agro, STLO, 35042, Rennes, France. E-mail:
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23
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Fernandes P, Loubens M, Marinach C, Coppée R, Baron L, Grand M, Andre TP, Hamada S, Langlois AC, Briquet S, Bun P, Silvie O. Plasmodium sporozoites require the protein B9 to invade hepatocytes. iScience 2023; 26:106056. [PMID: 36761022 PMCID: PMC9906020 DOI: 10.1016/j.isci.2023.106056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 11/16/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Plasmodium sporozoites are transmitted to a mammalian host during blood feeding by an infected mosquito and invade hepatocytes for initial replication of the parasite into thousands of erythrocyte-invasive merozoites. Here we report that the B9 protein, a member of the 6-cysteine domain protein family, is secreted from sporozoite micronemes and is required for productive invasion of hepatocytes. The N-terminus of B9 forms a beta-propeller domain structurally related to CyRPA, a cysteine-rich protein forming an essential invasion complex in Plasmodium falciparum merozoites. The beta-propeller domain of B9 is essential for sporozoite infectivity and interacts with the 6-cysteine proteins P36 and P52 in a heterologous expression system. Our results suggest that, despite using distinct sets of parasite and host entry factors, Plasmodium sporozoites and merozoites may share common structural modules to assemble protein complexes for invasion of host cells.
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Affiliation(s)
- Priyanka Fernandes
- Sorbonne Université, INSERM, CNRS, Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Paris, France
| | - Manon Loubens
- Sorbonne Université, INSERM, CNRS, Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Paris, France
| | - Carine Marinach
- Sorbonne Université, INSERM, CNRS, Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Paris, France
| | - Romain Coppée
- Université de Paris, UMR 261 MERIT, IRD, 75006 Paris, France
| | - Ludivine Baron
- Sorbonne Université, INSERM, CNRS, Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Paris, France
| | - Morgane Grand
- Sorbonne Université, INSERM, CNRS, Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Paris, France
| | - Thanh-Phuc Andre
- Sorbonne Université, INSERM, CNRS, Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Paris, France
| | - Soumia Hamada
- Sorbonne Université, INSERM, CNRS, Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Paris, France
- Sorbonne Université, INSERM, UMS PASS, Plateforme Post-génomique de la Pitié Salpêtrière (P3S), 75013 Paris, France
| | - Anne-Claire Langlois
- Sorbonne Université, INSERM, CNRS, Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Paris, France
| | - Sylvie Briquet
- Sorbonne Université, INSERM, CNRS, Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Paris, France
| | - Philippe Bun
- INSERM U1266, NeurImag Facility, Institute of Psychiatry and Neurosciences of Paris, Paris, France
| | - Olivier Silvie
- Sorbonne Université, INSERM, CNRS, Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Paris, France
- Corresponding author
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24
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Ghouili E, Sassi K, Hidri Y, M’Hamed HC, Somenahally A, Xue Q, Jebara M, Nefissi Ouertani R, Riahi J, de Oliveira AC, Abid G, Muhovski Y. Effects of Date Palm Waste Compost Application on Root Proteome Changes of Barley ( Hordeum vulgare L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:526. [PMID: 36771612 PMCID: PMC9921465 DOI: 10.3390/plants12030526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Proteomic analysis was performed to investigate the differentially abundant proteins (DAPs) in barley roots during the tillering stage. Bioinformatic tools were used to interpret the biological function, the pathway analysis and the visualisation of the network amongst the identified proteins. A total of 72 DAPs (33 upregulated and 39 downregulated) among a total of 2580 proteins were identified in response to compost treatment, suggesting multiple pathways of primary and secondary metabolism, such as carbohydrates and energy metabolism, phenylpropanoid pathway, glycolysis pathway, protein synthesis and degradation, redox homeostasis, RNA processing, stress response, cytoskeleton organisation, and phytohormone metabolic pathways. The expression of DAPs was further validated by qRT-PCR. The effects on barley plant development, such as the promotion of root growth and biomass increase, were associated with a change in energy metabolism and protein synthesis. The activation of enzymes involved in redox homeostasis and the regulation of stress response proteins suggest a protective effect of compost, consequently improving barley growth and stress acclimation through the reduction of the environmental impact of productive agriculture. Overall, these results may facilitate a better understanding of the molecular mechanism of compost-promoted plant growth and provide valuable information for the identification of critical genes/proteins in barley as potential targets of compost.
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Affiliation(s)
- Emna Ghouili
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Khaled Sassi
- Laboratory of Agronomy, National Agronomy Institute of Tunisia (INAT), University of Carthage, Avenue Charles Nicolle, Tunis-Mahrajène, P.O. Box 43, Tunis 1082, Tunisia
| | - Yassine Hidri
- Laboratory of Integrated Olive Production in the Humid, Sub-humid and Semi-arid Region (LR16IO3), Olive Tree Institute, Cité Mahragène, P.O. Box 208, Tunis 1082, Tunisia
| | - Hatem Cheikh M’Hamed
- Agronomy Laboratory, National Institute of Agronomic Research of Tunis (INRAT), Carthage University, Hedi Karray Street, Ariana 2049, Tunisia
| | - Anil Somenahally
- Department of Soil and Crop Sciences, Texas A&M University, 370 Olsen Blvd, College Station, TX 77843-2474, USA
| | - Qingwu Xue
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX 79403-6603, USA
| | - Moez Jebara
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Rim Nefissi Ouertani
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Jouhaina Riahi
- Laboratory of Agronomy, National Agronomy Institute of Tunisia (INAT), University of Carthage, Avenue Charles Nicolle, Tunis-Mahrajène, P.O. Box 43, Tunis 1082, Tunisia
| | - Ana Caroline de Oliveira
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, P.O. Box 234, 5030 Gembloux, Belgium
| | - Ghassen Abid
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Yordan Muhovski
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, P.O. Box 234, 5030 Gembloux, Belgium
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25
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Guillou MC, Balliau T, Vergne E, Canut H, Chourré J, Herrera-León C, Ramos-Martín F, Ahmadi-Afzadi M, D’Amelio N, Ruelland E, Zivy M, Renou JP, Jamet E, Aubourg S. The PROSCOOP10 Gene Encodes Two Extracellular Hydroxylated Peptides and Impacts Flowering Time in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2022; 11:3554. [PMID: 36559666 PMCID: PMC9784617 DOI: 10.3390/plants11243554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/29/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The Arabidopsis PROSCOOP genes belong to a family predicted to encode secreted pro-peptides, which undergo maturation steps to produce peptides named SCOOP. Some of them are involved in defence signalling through their perception by a receptor complex including MIK2, BAK1 and BKK1. Here, we focused on the PROSCOOP10 gene, which is highly and constitutively expressed in aerial organs. The MS/MS analyses of leaf apoplastic fluids allowed the identification of two distinct peptides (named SCOOP10#1 and SCOOP10#2) covering two different regions of PROSCOOP10. They both possess the canonical S-X-S family motif and have hydroxylated prolines. This identification in apoplastic fluids confirms the biological reality of SCOOP peptides for the first time. NMR and molecular dynamics studies showed that the SCOOP10 peptides, although largely unstructured in solution, tend to assume a hairpin-like fold, exposing the two serine residues previously identified as essential for the peptide activity. Furthermore, PROSCOOP10 mutations led to an early-flowering phenotype and increased expression of the floral integrators SOC1 and LEAFY, consistent with the de-regulated transcription of PROSCOOP10 in several other mutants displaying early- or late-flowering phenotypes. These results suggest a role for PROSCOOP10 in flowering time, highlighting the functional diversity within the PROSCOOP family.
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Affiliation(s)
| | - Thierry Balliau
- AgroParisTech, GQE—Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, F-91190 Gif-sur-Yvette, France
| | - Emilie Vergne
- Institut Agro, SFR QUASAV, IRHS, Université Angers, INRAE, F-49000 Angers, France
| | - Hervé Canut
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, Toulouse INP, CNRS, F-31320 Auzeville-Tolosane, France
| | - Josiane Chourré
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, Toulouse INP, CNRS, F-31320 Auzeville-Tolosane, France
| | - Claudia Herrera-León
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, F-80039 Amiens, France
| | - Francisco Ramos-Martín
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, F-80039 Amiens, France
| | - Masoud Ahmadi-Afzadi
- Institut Agro, SFR QUASAV, IRHS, Université Angers, INRAE, F-49000 Angers, France
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 117-76315, Iran
| | - Nicola D’Amelio
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, F-80039 Amiens, France
| | - Eric Ruelland
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Technologie de Compiègne, F-60203 Compiègne, France
| | - Michel Zivy
- AgroParisTech, GQE—Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, F-91190 Gif-sur-Yvette, France
| | - Jean-Pierre Renou
- Institut Agro, SFR QUASAV, IRHS, Université Angers, INRAE, F-49000 Angers, France
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, Toulouse INP, CNRS, F-31320 Auzeville-Tolosane, France
| | - Sébastien Aubourg
- Institut Agro, SFR QUASAV, IRHS, Université Angers, INRAE, F-49000 Angers, France
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26
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Smedile F, Foustoukos DI, Patwardhan S, Mullane K, Schlegel I, Adams MW, Schut GJ, Giovannelli D, Vetriani C. Adaptations to high pressure of Nautilia sp. strain PV-1, a piezophilic Campylobacterium (aka Epsilonproteobacterium) isolated from a deep-sea hydrothermal vent. Environ Microbiol 2022; 24:6164-6183. [PMID: 36271901 PMCID: PMC10092268 DOI: 10.1111/1462-2920.16256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/20/2022] [Indexed: 01/12/2023]
Abstract
Physiological and gene expression studies of deep-sea bacteria under pressure conditions similar to those experienced in their natural habitat are critical for understanding growth kinetics and metabolic adaptations to in situ conditions. The Campylobacterium (aka Epsilonproteobacterium) Nautilia sp. strain PV-1 was isolated from hydrothermal fluids released from an active deep-sea hydrothermal vent at 9° N on the East Pacific Rise. Strain PV-1 is a piezophilic, moderately thermophilic, chemolithoautotrophic anaerobe that conserves energy by coupling the oxidation of hydrogen to the reduction of nitrate or elemental sulfur. Using a high-pressure-high temperature continuous culture system, we established that strain PV-1 has the shortest generation time of all known piezophilic bacteria and we investigated its protein expression pattern in response to different hydrostatic pressure regimes. Proteogenomic analyses of strain PV-1 grown at 20 and 5 MPa showed that pressure adaptation is not restricted to stress response or homeoviscous adaptation but extends to enzymes involved in central metabolic pathways. Protein synthesis, motility, transport, and energy metabolism are all affected by pressure, although to different extents. In strain PV-1, low-pressure conditions induce the synthesis of phage-related proteins and an overexpression of enzymes involved in carbon fixation.
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Affiliation(s)
- Francesco Smedile
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA.,Institute of Polar Science (ISP-CNR), Messina, Italy
| | - Dionysis I Foustoukos
- Earth and Planets Laboratory, Carnegie Institution of Washington, Washington, District of Columbia, USA
| | - Sushmita Patwardhan
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Kelli Mullane
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA.,Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California, USA
| | - Ian Schlegel
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Michael W Adams
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Gerrit J Schut
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Donato Giovannelli
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA.,Department of Biology, University of Naples "Federico II", Naples, Italy
| | - Costantino Vetriani
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA.,Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
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27
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Leduc A, Le Guillou S, Bianchi L, Correia LO, Gelé M, Pires J, Martin P, Leroux C, Le Provost F, Boutinaud M. Milk proteins as a feed restriction signature indicating the metabolic adaptation of dairy cows. Sci Rep 2022; 12:18886. [PMID: 36344510 PMCID: PMC9640695 DOI: 10.1038/s41598-022-21804-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2022] Open
Abstract
Milk production in dairy cows is affected by numerous factors, including diet. Feed restriction is known to have little impact on milk total protein content but its effect on the fine protein composition is still poorly documented. The objective of this study was to describe the effects of two feed restriction trials of different intensities on the milk protein composition of Holstein cows. One restriction trial was of high intensity (H: 8 mid-lactation Holstein cows) and the second of moderate intensity (M: 19 peak lactation Holstein cows). Feed restriction decreased the milk protein yield for caseins under the M trial and of all six major milk proteins under the H trial. These decreased yields lead to lower concentrations of αs1-, αs2- and β-caseins during the H trial. The milk proteome, analyzed on 32 milk samples, was affected as a function of restriction intensity. Among the 345 proteins identified eight varied under the M trial and 160 under the H trial. Ontology analyses revealed their implication in carbohydrate, lipid and protein metabolisms as well as in the immune system. These proteins reflected adaptations of the animal and mammary gland physiology to feed restriction and constituted a signature of this change.
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Affiliation(s)
- A Leduc
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- INRAE, Institut Agro Rennes Angers, PEGASE, 35590, Saint-Gilles, France
- Institut de L'Elevage, 75012, Paris, France
| | - S Le Guillou
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - L Bianchi
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - L Oliveira Correia
- INRAE, AgroParisTech, Micalis Institute, PAPPSO, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - M Gelé
- Institut de L'Elevage, 75012, Paris, France
| | - J Pires
- INRAE, UMRH, Vetagro Sup, Université Clermont Auvergne, 63122, Saint-Genès-Champanelle, France
| | - P Martin
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - C Leroux
- INRAE, UMRH, Vetagro Sup, Université Clermont Auvergne, 63122, Saint-Genès-Champanelle, France
| | - F Le Provost
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - M Boutinaud
- INRAE, Institut Agro Rennes Angers, PEGASE, 35590, Saint-Gilles, France.
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28
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Wang J, Ossemond J, Jardin J, Briard-Bion V, Henry G, Le Gouar Y, Ménard O, Lê S, Madadlou A, Dupont D, Pédrono F. Encapsulation of DHA oil with heat-denatured whey protein in Pickering emulsion improves its bioaccessibility. Food Res Int 2022; 162:112112. [DOI: 10.1016/j.foodres.2022.112112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 11/05/2022]
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29
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Lebeau RH, Mendez-David I, Kucynski-Noyau L, Henry C, Attali D, Plaze M, Colle R, Corruble E, Gardier AM, Gaillard R, Guilloux JP, David DJ. Peripheral proteomic changes after electroconvulsive seizures in a rodent model of non-response to chronic fluoxetine. Front Pharmacol 2022; 13:993449. [DOI: 10.3389/fphar.2022.993449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/05/2022] [Indexed: 11/13/2022] Open
Abstract
Major depressive disorder (MDD) is the psychiatric disorder with the highest prevalence in the world. Pharmacological antidepressant treatment (AD), such as selective serotonin reuptake inhibitors [SSRI, i.e., fluoxetine (Flx)] is the first line of treatment for MDD. Despite its efficacy, lack of AD response occurs in numerous patients characterizing Difficult-to-treat Depression. ElectroConvulsive Therapy (ECT) is a highly effective treatment inducing rapid improvement in depressive symptoms and high remission rates of ∼50–63% in patients with pharmaco-resistant depression. Nevertheless, the need to develop reliable treatment response predictors to guide personalized AD strategies and supplement clinical observation is becoming a pressing clinical objective. Here, we propose to establish a proteomic peripheral biomarkers signature of ECT response in an anxio/depressive animal model of non-response to AD. Using an emotionality score based on the analysis complementary behavioral tests of anxiety/depression (Elevated Plus Maze, Novelty Suppressed Feeding, Splash Test), we showed that a 4-week corticosterone treatment (35 μg/ml, Cort model) in C57BL/6JRj male mice induced an anxiety/depressive-like behavior. A 28-day chronic fluoxetine treatment (Flx, 18 mg/kg/day) reduced corticosterone-induced increase in emotional behavior. A 50% decrease in emotionality score threshold before and after Flx, was used to separate Flx-responding mice (Flx-R, n = 18), or Flx non-responder mice (Flx-NR, n = 7). Then, Flx-NR mice received seven sessions of electroconvulsive seizure (ECS, equivalent to ECT in humans) and blood was collected before and after ECS treatment. Chronic ECS normalized the elevated emotionality observed in Flx-NR mice. Then, proteins were extracted from peripheral blood mononuclear cells (PBMCs) and isolated for proteomic analysis using a high-resolution MS Orbitrap. Data are available via ProteomeXchange with identifier PXD037392. The proteomic analysis revealed a signature of 33 peripheral proteins associated with response to ECS (7 down and 26 upregulated). These proteins were previously associated with mental disorders and involved in regulating pathways which participate to the depressive disorder etiology.
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30
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de Nies L, Busi SB, Kunath BJ, May P, Wilmes P. Mobilome-driven segregation of the resistome in biological wastewater treatment. eLife 2022; 11:81196. [PMID: 36111782 PMCID: PMC9643006 DOI: 10.7554/elife.81196] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/15/2022] [Indexed: 12/05/2022] Open
Abstract
Biological wastewater treatment plants (BWWTP) are considered to be hotspots for the evolution and subsequent spread of antimicrobial resistance (AMR). Mobile genetic elements (MGEs) promote the mobilization and dissemination of antimicrobial resistance genes (ARGs) and are thereby critical mediators of AMR within the BWWTP microbial community. At present, it is unclear whether specific AMR categories are differentially disseminated via bacteriophages (phages) or plasmids. To understand the segregation of AMR in relation to MGEs, we analyzed meta-omic (metagenomic, metatranscriptomic and metaproteomic) data systematically collected over 1.5 years from a BWWTP. Our results showed a core group of 15 AMR categories which were found across all timepoints. Some of these AMR categories were disseminated exclusively (bacitracin) or primarily (aminoglycoside, MLS and sulfonamide) via plasmids or phages (fosfomycin and peptide), whereas others were disseminated equally by both. Combined and timepoint-specific analyses of gene, transcript and protein abundances further demonstrated that aminoglycoside, bacitracin and sulfonamide resistance genes were expressed more by plasmids, in contrast to fosfomycin and peptide AMR expression by phages, thereby validating our genomic findings. In the analyzed communities, the dominant taxon Candidatus Microthrix parvicella was a major contributor to several AMR categories whereby its plasmids primarily mediated aminoglycoside resistance. Importantly, we also found AMR associated with ESKAPEE pathogens within the BWWTP, and here MGEs also contributed differentially to the dissemination of the corresponding ARGs. Collectively our findings pave the way toward understanding the segmentation of AMR within MGEs, thereby shedding new light on resistome populations and their mediators, essential elements that are of immediate relevance to human health.
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Affiliation(s)
- Laura de Nies
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg
| | | | | | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg
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31
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da Luz BSR, de Rezende Rodovalho V, Nicolas A, Chabelskaya S, Jardin J, Briard-Bion V, Le Loir Y, de Carvalho Azevedo VA, Guédon É. Impact of Environmental Conditions on the Protein Content of Staphylococcus aureus and Its Derived Extracellular Vesicles. Microorganisms 2022; 10:1808. [PMID: 36144410 PMCID: PMC9506334 DOI: 10.3390/microorganisms10091808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/01/2022] [Accepted: 09/04/2022] [Indexed: 12/03/2022] Open
Abstract
Staphylococcus aureus, a major opportunistic pathogen in humans, produces extracellular vesicles (EVs) that are involved in cellular communication, the delivery of virulence factors, and modulation of the host immune system response. However, to date, the impact of culture conditions on the physicochemical and functional properties of S. aureus EVs is still largely unexplored. Here, we use a proteomic approach to provide a complete protein characterization of S. aureus HG003, a NCTC8325 derivative strain and its derived EVs under four growth conditions: early- and late-stationary growth phases, and in the absence and presence of a sub-inhibitory concentration of vancomycin. The HG003 EV protein composition in terms of subcellular localization, COG and KEGG categories, as well as their relative abundance are modulated by the environment and differs from that of whole-cell (WC). Moreover, the environmental conditions that were tested had a more pronounced impact on the EV protein composition when compared to the WC, supporting the existence of mechanisms for the selective packing of EV cargo. This study provides the first general picture of the impact of different growth conditions in the proteome of S. aureus EVs and its producing-cells and paves the way for future studies to understand better S. aureus EV production, composition, and roles.
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Affiliation(s)
- Brenda Silva Rosa da Luz
- INRAE, Institut Agro, STLO, F-35000 Rennes, France
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Vinícius de Rezende Rodovalho
- INRAE, Institut Agro, STLO, F-35000 Rennes, France
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | | | - Svetlana Chabelskaya
- BRM (Bacterial Regulatory RNAs and Medicine) UMR_S 1230, Inserm 1230, University of Rennes 1, 35000 Rennes, France
| | | | | | - Yves Le Loir
- INRAE, Institut Agro, STLO, F-35000 Rennes, France
| | - Vasco Ariston de Carvalho Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Éric Guédon
- INRAE, Institut Agro, STLO, F-35000 Rennes, France
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32
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Label-Free Quantitative Proteomics Reveal the Involvement of PRT6 in Arabidopsis thaliana Seed Responsiveness to Ethylene. Int J Mol Sci 2022; 23:ijms23169352. [PMID: 36012613 PMCID: PMC9409418 DOI: 10.3390/ijms23169352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
In Arabidopsis thaliana, the breaking of seed dormancy in wild type (Col-0) by ethylene at 100 μL L-1 required at least 30 h application. A mutant of the proteolytic N-degron pathway, lacking the E3 ligase PROTEOLYSIS 6 (PRT6), was investigated for its role in ethylene-triggered changes in proteomes during seed germination. Label-free quantitative proteomics was carried out on dormant wild type Col-0 and prt6 seeds treated with (+) or without (-) ethylene. After 16 h, 1737 proteins were identified, but none was significantly different in protein levels in response to ethylene. After longer ethylene treatment (30 h), 2552 proteins were identified, and 619 Differentially Expressed Proteins (DEPs) had significant differences in protein abundances between ethylene treatments and genotypes. In Col, 587 DEPs were enriched for those involved in signal perception and transduction, reserve mobilization and new material generation, which potentially contributed to seed germination. DEPs up-regulated by ethylene in Col included S-adenosylmethionine synthase 1, methionine adenosyltransferase 3 and ACC oxidase involved in ethylene synthesis and of Pyrabactin Resistance1 acting as an ABA receptor, while DEPs down-regulated by ethylene in Col included aldehyde oxidase 4 involved in ABA synthesis. In contrast, in prt6 seeds, ethylene did not result in strong proteomic changes with only 30 DEPs. Taken together, the present work demonstrates that the proteolytic N-degron pathway is essential for ethylene-mediated reprogramming of seed proteomes during germination.
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33
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Peslerbes M, Fellenberg A, Jardin J, Deglaire A, Ibáñez RA. Manufacture of Whey Protein Hydrolysates Using Plant Enzymes: Effect of Processing Conditions and Simulated Gastrointestinal Digestion on Angiotensin-I-Converting Enzyme (ACE) Inhibitory Activity. Foods 2022; 11:2429. [PMID: 36010429 PMCID: PMC9407499 DOI: 10.3390/foods11162429] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/03/2022] [Accepted: 08/08/2022] [Indexed: 11/19/2022] Open
Abstract
Hydrolysis of proteins leads to the release of bioactive peptides with positive impact on human health. Peptides exhibiting antihypertensive properties (i.e., inhibition of angiotensin-I-converting enzyme) are commonly found in whey protein hydrolysates made with enzymes of animal, plant or microbial origin. However, bioactive properties can be influenced by processing conditions and gastrointestinal digestion. In this study, we evaluated the impact of three plant enzymes (papain, bromelain and ficin) in the manufacture of whey protein hydrolysates with varying level of pH, enzyme-to-substrate ratio and time of hydrolysis, based on a central composite design, to determine the degree of hydrolysis and antihypertensive properties. Hydrolysates made on laboratory scales showed great variation in the type of enzyme used, their concentrations and the pH level of hydrolysis. However, low degrees of hydrolysis in papain and bromelain treatments were associated with increased antihypertensive properties, when compared to ficin. Simulated gastrointestinal digestion performed for selected hydrolysates showed an increase in antihypertensive properties of hydrolysates made with papain and bromelain, which was probably caused by further release of peptides. Several peptides with reported antihypertensive properties were found in all treatments. These results suggest plant enzymes used in this study can be suitable candidates to develop ingredients with bioactive properties.
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Affiliation(s)
- Marie Peslerbes
- Departamento de Ciencias Animales, Facultad de Agronomia e Ingenieria Forestal, Pontificia Universidad Catolica de Chile, Macul, Santiago 7820436, Chile
- École Supérieure D’agricultures Angers Loire, 49000 Angers, France
| | - Angélica Fellenberg
- Departamento de Ciencias Animales, Facultad de Agronomia e Ingenieria Forestal, Pontificia Universidad Catolica de Chile, Macul, Santiago 7820436, Chile
| | | | | | - Rodrigo A. Ibáñez
- Departamento de Ciencias Animales, Facultad de Agronomia e Ingenieria Forestal, Pontificia Universidad Catolica de Chile, Macul, Santiago 7820436, Chile
- Center for Dairy Research, University of Wisconsin-Madison, Madison, WI 53706, USA
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34
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 11/26/2022]
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35
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Domenzain I, Sánchez B, Anton M, Kerkhoven EJ, Millán-Oropeza A, Henry C, Siewers V, Morrissey JP, Sonnenschein N, Nielsen J. Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0. Nat Commun 2022; 13:3766. [PMID: 35773252 PMCID: PMC9246944 DOI: 10.1038/s41467-022-31421-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/16/2022] [Indexed: 01/08/2023] Open
Abstract
Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration of enzyme constraints and proteomics data into such models was first enabled by the GECKO toolbox, allowing the study of phenotypes constrained by protein limitations. Here, we upgrade the toolbox in order to enhance models with enzyme and proteomics constraints for any organism with a compatible GEM reconstruction. With this, enzyme-constrained models for the budding yeasts Saccharomyces cerevisiae, Yarrowia lipolytica and Kluyveromyces marxianus are generated to study their long-term adaptation to several stress factors by incorporation of proteomics data. Predictions reveal that upregulation and high saturation of enzymes in amino acid metabolism are common across organisms and conditions, suggesting the relevance of metabolic robustness in contrast to optimal protein utilization as a cellular objective for microbial growth under stress and nutrient-limited conditions. The functionality of GECKO is expanded with an automated framework for continuous and version-controlled update of enzyme-constrained GEMs, also producing such models for Escherichia coli and Homo sapiens. In this work, we facilitate the utilization of enzyme-constrained GEMs in basic science, metabolic engineering and synthetic biology purposes.
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Affiliation(s)
- Iván Domenzain
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Benjamín Sánchez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Mihail Anton
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Kemivägen 10, SE-412 58, Gothenburg, Sweden
| | - Eduard J Kerkhoven
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Aarón Millán-Oropeza
- Plateforme d'analyse protéomique Paris Sud-Ouest (PAPPSO), INRAE, MICALIS Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Céline Henry
- Plateforme d'analyse protéomique Paris Sud-Ouest (PAPPSO), INRAE, MICALIS Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - John P Morrissey
- School of Microbiology, Environmental Research Institute and APC Microbiome Ireland, University College Cork, T12 K8AF, Cork, Ireland
| | - Nikolaus Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
- BioInnovation Institute, Ole Maaløes Vej 3, 2200, Copenhagen, Denmark.
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Plancade S, Berland M, Blein-Nicolas M, Langella O, Bassignani A, Juste C. A combined test for feature selection on sparse metaproteomics data-an alternative to missing value imputation. PeerJ 2022; 10:e13525. [PMID: 35769140 PMCID: PMC9235818 DOI: 10.7717/peerj.13525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 05/11/2022] [Indexed: 01/18/2023] Open
Abstract
One of the difficulties encountered in the statistical analysis of metaproteomics data is the high proportion of missing values, which are usually treated by imputation. Nevertheless, imputation methods are based on restrictive assumptions regarding missingness mechanisms, namely "at random" or "not at random". To circumvent these limitations in the context of feature selection in a multi-class comparison, we propose a univariate selection method that combines a test of association between missingness and classes, and a test for difference of observed intensities between classes. This approach implicitly handles both missingness mechanisms. We performed a quantitative and qualitative comparison of our procedure with imputation-based feature selection methods on two experimental data sets, as well as simulated data with various scenarios regarding the missingness mechanisms and the nature of the difference of expression (differential intensity or differential presence). Whereas we observed similar performances in terms of prediction on the experimental data set, the feature ranking and selection from various imputation-based methods were strongly divergent. We showed that the combined test reaches a compromise by correlating reasonably with other methods, and remains efficient in all simulated scenarios unlike imputation-based feature selection methods.
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Affiliation(s)
- Sandra Plancade
- UR875 MIAT, Université fédérale de Toulouse, INRAE, Castanet-Tolosan, France
| | - Magali Berland
- Université Paris-Saclay, INRAE, MGP, Jouy en Josas, France
| | - Mélisande Blein-Nicolas
- Université Paris-Saclay, CNRS, INRAE, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette, France,Université Paris-Saclay, CNRS, INRAE, AgroParisTech, PAPPSO, Gif-sur-Yvette, France
| | - Olivier Langella
- Université Paris-Saclay, CNRS, INRAE, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette, France,Université Paris-Saclay, CNRS, INRAE, AgroParisTech, PAPPSO, Gif-sur-Yvette, France
| | - Ariane Bassignani
- Université Paris-Saclay, INRAE, MGP, Jouy en Josas, France,Université Paris-Saclay, CNRS, INRAE, AgroParisTech, PAPPSO, Gif-sur-Yvette, France
| | - Catherine Juste
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParis Tech, Jouy-en-Josas, France
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37
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Baudouin E, Puyaubert J, Meimoun P, Blein-Nicolas M, Davanture M, Zivy M, Bailly C. Dynamics of Protein Phosphorylation during Arabidopsis Seed Germination. Int J Mol Sci 2022; 23:ijms23137059. [PMID: 35806063 PMCID: PMC9266807 DOI: 10.3390/ijms23137059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022] Open
Abstract
Seed germination is critical for early plantlet development and is tightly controlled by environmental factors. Nevertheless, the signaling networks underlying germination control remain elusive. In this study, the remodeling of Arabidopsis seed phosphoproteome during imbibition was investigated using stable isotope dimethyl labeling and nanoLC-MS/MS analysis. Freshly harvested seeds were imbibed under dark or constant light to restrict or promote germination, respectively. For each light regime, phosphoproteins were extracted and identified from dry and imbibed (6 h, 16 h, and 24 h) seeds. A large repertoire of 10,244 phosphopeptides from 2546 phosphoproteins, including 110 protein kinases and key regulators of seed germination such as Delay Of Germination 1 (DOG1), was established. Most phosphoproteins were only identified in dry seeds. Early imbibition led to a similar massive downregulation in dormant and non-dormant seeds. After 24 h, 411 phosphoproteins were specifically identified in non-dormant seeds. Gene ontology analyses revealed their involvement in RNA and protein metabolism, transport, and signaling. In addition, 489 phosphopeptides were quantified, and 234 exhibited up or downregulation during imbibition. Interaction networks and motif analyses revealed their association with potential signaling modules involved in germination control. Our study provides evidence of a major role of phosphosignaling in the regulation of Arabidopsis seed germination.
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Affiliation(s)
- Emmanuel Baudouin
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
- Correspondence: ; Tel.: +33-1-44-27-59-87
| | - Juliette Puyaubert
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
| | - Patrice Meimoun
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
| | - Mélisande Blein-Nicolas
- PAPPSO, Génétique Quantitative et Evolution (GQE), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, F-91190 Gif-sur-Yvette, France; (M.B.-N.); (M.D.); (M.Z.)
| | - Marlène Davanture
- PAPPSO, Génétique Quantitative et Evolution (GQE), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, F-91190 Gif-sur-Yvette, France; (M.B.-N.); (M.D.); (M.Z.)
| | - Michel Zivy
- PAPPSO, Génétique Quantitative et Evolution (GQE), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, F-91190 Gif-sur-Yvette, France; (M.B.-N.); (M.D.); (M.Z.)
| | - Christophe Bailly
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
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38
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Spaan AN, Neehus AL, Laplantine E, Staels F, Ogishi M, Seeleuthner Y, Rapaport F, Lacey KA, Van Nieuwenhove E, Chrabieh M, Hum D, Migaud M, Izmiryan A, Lorenzo L, Kochetkov T, Heesterbeek DAC, Bardoel BW, DuMont AL, Dobbs K, Chardonnet S, Heissel S, Baslan T, Zhang P, Yang R, Bogunovic D, Wunderink HF, Haas PJA, Molina H, Van Buggenhout G, Lyonnet S, Notarangelo LD, Seppänen MRJ, Weil R, Seminario G, Gomez-Tello H, Wouters C, Mesdaghi M, Shahrooei M, Bossuyt X, Sag E, Topaloglu R, Ozen S, Leavis HL, van Eijk MMJ, Bezrodnik L, Blancas Galicia L, Hovnanian A, Nassif A, Bader-Meunier B, Neven B, Meyts I, Schrijvers R, Puel A, Bustamante J, Aksentijevich I, Kastner DL, Torres VJ, Humblet-Baron S, Liston A, Abel L, Boisson B, Casanova JL. Human OTULIN haploinsufficiency impairs cell-intrinsic immunity to staphylococcal α-toxin. Science 2022; 376:eabm6380. [PMID: 35587511 PMCID: PMC9233084 DOI: 10.1126/science.abm6380] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The molecular basis of interindividual clinical variability upon infection with Staphylococcus aureus is unclear. We describe patients with haploinsufficiency for the linear deubiquitinase OTULIN, encoded by a gene on chromosome 5p. Patients suffer from episodes of life-threatening necrosis, typically triggered by S. aureus infection. The disorder is phenocopied in patients with the 5p- (Cri-du-Chat) chromosomal deletion syndrome. OTULIN haploinsufficiency causes an accumulation of linear ubiquitin in dermal fibroblasts, but tumor necrosis factor receptor-mediated nuclear factor κB signaling remains intact. Blood leukocyte subsets are unaffected. The OTULIN-dependent accumulation of caveolin-1 in dermal fibroblasts, but not leukocytes, facilitates the cytotoxic damage inflicted by the staphylococcal virulence factor α-toxin. Naturally elicited antibodies against α-toxin contribute to incomplete clinical penetrance. Human OTULIN haploinsufficiency underlies life-threatening staphylococcal disease by disrupting cell-intrinsic immunity to α-toxin in nonleukocytic cells.
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Affiliation(s)
- András N Spaan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Anna-Lena Neehus
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
- Institute of Experimental Hematology, REBIRTH Research Center for Translational and Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Emmanuel Laplantine
- Centre d'Immunologie et des Maladies Infectieuses, INSERM U1135, CNRS ERL8255, Sorbonne University, 75724 Paris, France
- Institut de Recherche St. Louis, Hôpital St. Louis, INSERM U944, CNRS U7212, Paris Cité University, 75010 Paris, France
| | - Frederik Staels
- Laboratory for Adaptive Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
| | - Franck Rapaport
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Keenan A Lacey
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Erika Van Nieuwenhove
- Laboratory for Adaptive Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
- Department of Pediatric Rheumatology and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Maya Chrabieh
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
| | - David Hum
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
| | - Araksya Izmiryan
- Imagine Institute, Paris Cité University, 75015 Paris, France
- Laboratory of Genetic Skin Diseases, INSERM U1163, 75015 Paris, France
| | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
| | - Tatiana Kochetkov
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Dani A C Heesterbeek
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Bart W Bardoel
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Ashley L DuMont
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD 20852, USA
| | - Solenne Chardonnet
- Plateforme Post-génomique de la Pitié-Salpêtrière, P3S, UMS Production et Analyse de données en Sciences de la vie et en Santé, PASS, INSERM, Sorbonne University, 75013 Paris, France
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Rui Yang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Dusan Bogunovic
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Herman F Wunderink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Pieter-Jan A Haas
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Griet Van Buggenhout
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Stanislas Lyonnet
- Imagine Institute, Paris Cité University, 75015 Paris, France
- Laboratory Embryology and Genetics of Malformations, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD 20852, USA
| | - Mikko R J Seppänen
- Rare Disease and Pediatric Research Centers, Children and Adolescents, University of Helsinki and HUS Helsinki University Hospital, 00260 Helsinki, Finland
| | - Robert Weil
- Centre d'Immunologie et des Maladies Infectieuses, INSERM U1135, CNRS ERL8255, Sorbonne University, 75724 Paris, France
| | - Gisela Seminario
- Center for Clinical Immunology, Immunology Group Children's Hospital Ricardo Gutiérrez, C1425EFD Buenos Aires, Argentina
| | - Héctor Gomez-Tello
- Immunology Department, Poblano Children's Hospital, 72190 Puebla, Mexico
| | - Carine Wouters
- Laboratory for Adaptive Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
- Department of Pediatrics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Mehrnaz Mesdaghi
- Department of Allergy and Clinical Immunology, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, 15468-155514 Tehran, Iran
| | - Mohammad Shahrooei
- Clinical and Diagnostic Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
- Specialized Immunology Laboratory of Dr. Shahrooei, Sina Medical Complex, 15468-155514 Ahvaz, Iran
| | - Xavier Bossuyt
- Clinical and Diagnostic Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Erdal Sag
- Department of Pediatric Rheumatology, Hacettepe University, 06230 Ankara, Turkey
| | - Rezan Topaloglu
- Department of Pediatric Nephrology, Hacettepe University School of Medicine, Hacettepe University, 06230 Ankara, Turkey
| | - Seza Ozen
- Department of Pediatric Rheumatology, Hacettepe University, 06230 Ankara, Turkey
| | - Helen L Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Maarten M J van Eijk
- Department of Intensive Care Medicine, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Liliana Bezrodnik
- Center for Clinical Immunology, Immunology Group Children's Hospital Ricardo Gutiérrez, C1425EFD Buenos Aires, Argentina
| | | | - Alain Hovnanian
- Imagine Institute, Paris Cité University, 75015 Paris, France
- Laboratory of Genetic Skin Diseases, INSERM U1163, 75015 Paris, France
- Department of Genetics, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France
| | - Aude Nassif
- Centre Médical, Institut Pasteur, 75724 Paris, France
| | - Brigitte Bader-Meunier
- Imagine Institute, Paris Cité University, 75015 Paris, France
- Pediatric Immunology, Hematology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France
- Laboratory of Immunogenetics of Pediatric Autoimmunity, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
| | - Bénédicte Neven
- Imagine Institute, Paris Cité University, 75015 Paris, France
- Pediatric Immunology, Hematology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France
- Laboratory of Immunogenetics of Pediatric Autoimmunity, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
| | - Isabelle Meyts
- Laboratory of Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
- Department of Pediatrics, Jeffrey Modell Diagnostic and Research Network Center, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Rik Schrijvers
- Allergy and Clinical Immunology Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France
| | - Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Daniel L Kastner
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Victor J Torres
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Stéphanie Humblet-Baron
- Laboratory for Adaptive Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Adrian Liston
- Laboratory for Adaptive Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
- VIB Center for Brain and Disease Research, Leuven 3000, Belgium
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
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Gagnaire V, Lecomte X, Richoux R, Genay M, Jardin J, Briard-Bion V, Kerjean JR, Thierry A. Little Impact of NaCl Reduction in Swiss-Type Cheese. Front Nutr 2022; 9:888179. [PMID: 35782920 PMCID: PMC9243640 DOI: 10.3389/fnut.2022.888179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/20/2022] [Indexed: 11/29/2022] Open
Abstract
Reducing salt intake can mitigate the prevalence of metabolic disorders. In fermented foods such as cheeses, however, salt can impact the activity of desirable and undesirable microorganisms and thus affect their properties. This study aimed to investigate the effect of salt level on Swiss-type cheese ripening. Since proteolysis is a major event in cheese ripening, three strains of Lactobacillus helveticus were selected on the cell-envelope proteinase (CEP) they harbor. Their proteolytic activity on caseins was studied at six salt levels (0–4.5%) at pH 7.5 and 5.2. Swiss-type cheeses were manufactured at regular, increased, and decreased salt concentrations, and characterized for their composition and techno-functional properties. L. helveticus strains possessed and expressed the expected CEPs, as shown by PCR and shaving experiments. The two strains of L. helveticus that possessed at least the CEP PrtH3 showed the greatest proteolytic activity. Casein hydrolysis in vitro was similar or higher at pH 5.2, i.e., cheese pH, compared to pH 7.5, and slightly decreased at the highest salt concentrations (3.0 and 4.4%). Similarly, in ripened cheeses, these L. helveticus strains showed 1.5–2.4 more proteolysis, compared to the cheeses manufactured without L. helveticus. Regarding the salt effect, the 30% salt-reduced cheeses showed the same proteolysis as regular cheeses, while the upper-salted cheeses showed a slight decrease (−14%) of the non-protein fraction. The microbial and biochemical composition remained unchanged in the 30%-reduced cheeses. In contrast, Propionibacterium freudenreichii, used as ripening bacteria in Swiss cheese, grew more slowly in upper-salted (1.14%, w/w) cheeses, which induced concomitant changes in the metabolites they consumed (−40% lactic acid) or produced (fivefold decrease in propionic acid). Some cheese techno-functional properties were slightly decreased by salt reduction, as extrusion (−17%) and oiling off (−4%) compared to regular cheeses. Overall, this study showed that a 30% salt reduction has little impact in the properties of Swiss-type cheeses, and that starters and ripening cultures strains could be chosen to compensate changes induced by salt modifications in Swiss-type and other hard cheeses.
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Affiliation(s)
- Valérie Gagnaire
- UMR STLO, INRAE, Institut Agro, Rennes, France
- *Correspondence: Valérie Gagnaire,
| | - Xavier Lecomte
- UMR STLO, INRAE, Institut Agro, Rennes, France
- CALBINOTOX, Université de Lorraine, Nancy, France
| | | | - Magali Genay
- CALBINOTOX, Université de Lorraine, Nancy, France
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40
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Sano N, Lounifi I, Cueff G, Collet B, Clément G, Balzergue S, Huguet S, Valot B, Galland M, Rajjou L. Multi-Omics Approaches Unravel Specific Features of Embryo and Endosperm in Rice Seed Germination. FRONTIERS IN PLANT SCIENCE 2022; 13:867263. [PMID: 35755645 PMCID: PMC9225960 DOI: 10.3389/fpls.2022.867263] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Seed germination and subsequent seedling growth affect the final yield and quality of the crop. Seed germination is defined as a series of processes that begins with water uptake by a quiescent dry seed and ends with the elongation of embryonic axis. Rice is an important cereal crop species, and during seed germination, two tissues function in a different manner; the embryo grows into a seedling as the next generation and the endosperm is responsible for nutritional supply. Toward understanding the integrated roles of each tissue at the transcriptional, translational, and metabolic production levels during germination, an exhaustive "multi-omics" analysis was performed by combining transcriptomics, label-free shotgun proteomics, and metabolomics on rice germinating embryo and endosperm, independently. Time-course analyses of the transcriptome and metabolome in germinating seeds revealed a major turning point in the early phase of germination in both embryo and endosperm, suggesting that dramatic changes begin immediately after water imbibition in the rice germination program at least at the mRNA and metabolite levels. In endosperm, protein profiles mostly showed abundant decreases corresponding to 90% of the differentially accumulated proteins. An ontological classification revealed the shift from the maturation to the germination process where over-represented classes belonged to embryonic development and cellular amino acid biosynthetic processes. In the embryo, 19% of the detected proteins are differentially accumulated during germination. Stress response, carbohydrate, fatty acid metabolism, and transport are the main functional classes representing embryo proteome change. Moreover, proteins specific to the germinated state were detected by both transcriptomic and proteomic approaches and a major change in the network operating during rice germination was uncovered. In particular, concomitant changes of hormonal metabolism-related proteins (GID1L2 and CNX1) implicated in GAs and ABA metabolism, signaling proteins, and protein turnover events emphasized the importance of such biological networks in rice seeds. Using metabolomics, we highlighted the importance of an energetic supply in rice seeds during germination. In both embryo and endosperm, starch degradation, glycolysis, and subsequent pathways related to these cascades, such as the aspartate-family pathway, are activated during germination. A relevant number of accumulated proteins and metabolites, especially in embryos, testifies the pivotal role of energetic supply in the preparation of plant growth. This article summarizes the key genetic pathways in embryo and endosperm during rice seed germination at the transcriptional, translational, and metabolite levels and thereby, emphasizes the value of combined multi-omics approaches to uncover the specific feature of tissues during germination.
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Affiliation(s)
- Naoto Sano
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Imen Lounifi
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
- MBCC Group, Master Builders Construction Chemical, Singapore, Singapore
| | - Gwendal Cueff
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Boris Collet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Gilles Clément
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Sandrine Balzergue
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
| | - Stéphanie Huguet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Benoît Valot
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, PAPPSO, Plateforme d'Analyse de Proteomique Paris-Sud-Ouest, Gif-sur-Yvette, France
- Chrono-Environnement Research Team UMR/CNRS-6249, Bourgogne-Franche-Comté University, Besançon, France
| | - Marc Galland
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Loïc Rajjou
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
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Hogrel G, Marino-Puertas L, Laurent S, Ibrahim Z, Covès J, Girard E, Gabel F, Fenel D, Daugeron MC, Clouet-d'Orval B, Basta T, Flament D, Franzetti B. Characterization of a small tRNA-binding protein that interacts with the archaeal proteasome complex. Mol Microbiol 2022; 118:16-29. [PMID: 35615908 PMCID: PMC9540759 DOI: 10.1111/mmi.14948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 11/27/2022]
Abstract
The proteasome system allows the elimination of functional or structurally impaired proteins. This includes the degradation of nascent peptides. In Archaea, how the proteasome complex interacts with the translational machinery remains to be described. Here, we characterised a small orphan protein, Q9UZY3 (Uniprot ID) conserved in Thermococcales. The protein was identified in native pull-down experiments using the proteasome regulatory complex (PAN) as bait. X-ray crystallography and SAXS experiments revealed that the protein is monomeric and adopts a β-barrel core structure with an Oligonucleotide/oligosaccharide-Binding (OB) fold, typically found in translation elongation factors. Mobility shift experiment showed that Q9UZY3 displays tRNA binding properties. Pull-downs, co-immunoprecipitation and ITC studies revealed that Q9UZY3 interacts in vitro with PAN. Native pull-downs and proteomic analysis using different versions of Q9UZY3 showed that the protein interacts with the assembled PAN-20S proteasome machinery in Pyrococcus abyssi cellular extracts. The protein was therefore named Pbp11, for Proteasome Binding Protein of 11 kDa. Interestingly, the interaction network of Pbp11 also includes ribosomal proteins, tRNA processing enzymes and exosome subunits dependent on Pbp11's N-terminal domain that was found to be essential for tRNA binding. Together these data suggest that Pbp11 participates in an interface between the proteasome and the translational machinery.
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Affiliation(s)
- Gaëlle Hogrel
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.,University of St Andrews, St Andrews, UK
| | | | - Sébastien Laurent
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Ziad Ibrahim
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.,University of Leicester, Leicester, UK
| | - Jacques Covès
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Eric Girard
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Frank Gabel
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Daphna Fenel
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Marie-Claire Daugeron
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Béatrice Clouet-d'Orval
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Tamara Basta
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Didier Flament
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
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Gérard C, Thébault M, Lamarthée B, Genet C, Cattin F, Brazdova A, Janikashvili N, Cladière C, Ciudad M, Ouandji S, Ghesquière T, Greigert H, Tinel C, Adotevi O, Saas P, Samson M, Audia S, Bonnotte B. Human Monocyte-Derived Suppressor Cell Supernatant Induces Immunoregulatory Effects and Mitigates xenoGvHD. Front Immunol 2022; 13:827712. [PMID: 35345675 PMCID: PMC8957111 DOI: 10.3389/fimmu.2022.827712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/11/2022] [Indexed: 12/03/2022] Open
Abstract
Recently developed cell-based therapies have shown potential for graft-versus-host disease (GvHD) mitigation. Our team previously developed a protocol to generate human monocyte-derived suppressor Cells (HuMoSC), a subpopulation of CD33+ suppressor cells of monocytic origin. CD33+HuMoSC successfully reduced xenoGvHD severity in NOD/SCID/IL-2Rγc-/- (NSG) mice. While CD33+ HuMoSC culture supernatant inhibits T cell activation and proliferation, the recovery of CD33+ HuMoSC immunosuppressive cells and the subsequent production of their supernatant is limited. An attractive solution would be to use both the CD33+ and the large number of CD14+ cells derived from our protocol. Here, we assessed the immunoregulatory properties of the CD14+HuMoSC supernatant and demonstrated that it inhibited both CD4 and CD8 T cell proliferation and decreased CD8 cytotoxicity. In vivo, injection of CD14+HuMoSC supernatant reduced xenoGvHD in NSG mice. Furthermore, CD14+HuMoSC supernatant maintained its immunoregulatory properties in an inflammatory environment. Proteomic and multiplex analyses revealed the presence of immunosuppressive proteins such as GPNMB, galectin-3 and IL-1R(A) Finally, CD14+HuMoSC supernatant can be produced using good manufacturing practices and be used as complement to current immunosuppressive drugs. CD14+HuMoSC supernatant is thus a promising therapy for preventing GvHD.
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Affiliation(s)
- Claire Gérard
- Université Bourgogne Franche-Comté (UBFC), Inserm, EFS BFC, UMR1098, Team « immunoregulation, immunopathology », RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France.,Department of Internal Medicine, Dijon University Hospital, Dijon, France
| | - Marine Thébault
- Université Bourgogne Franche-Comté (UBFC), Inserm, EFS BFC, UMR1098, Team « immunoregulation, immunopathology », RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France
| | - Baptiste Lamarthée
- Université Bourgogne Franche-Comté (UBFC), Inserm, EFS BFC, UMR1098, Team « immunoregulation, immunopathology », RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France
| | - Coraline Genet
- Université Bourgogne Franche-Comté (UBFC), Inserm, EFS BFC, UMR1098, Team « immunoregulation, immunopathology », RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France
| | - Florine Cattin
- Université Bourgogne Franche-Comté (UBFC), Inserm, EFS BFC, UMR1098, Team « immunoregulation, immunopathology », RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France
| | - Andréa Brazdova
- Université Bourgogne Franche-Comté (UBFC), Inserm, EFS BFC, UMR1098, Team « immunoregulation, immunopathology », RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czechia
| | - Nona Janikashvili
- Université Bourgogne Franche-Comté (UBFC), Inserm, EFS BFC, UMR1098, Team « immunoregulation, immunopathology », RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France.,Department of Immunology, Faculty of Medicine, Tbilisi State Medical University (TSMU), Tbilisi, Georgia
| | - Claudie Cladière
- Université Bourgogne Franche-Comté (UBFC), Inserm, EFS BFC, UMR1098, Team « immunoregulation, immunopathology », RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France
| | - Marion Ciudad
- Université Bourgogne Franche-Comté (UBFC), Inserm, EFS BFC, UMR1098, Team « immunoregulation, immunopathology », RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France
| | - Séthi Ouandji
- Université Bourgogne Franche-Comté (UBFC), Inserm, EFS BFC, UMR1098, Team « immunoregulation, immunopathology », RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France
| | - Thibault Ghesquière
- Université Bourgogne Franche-Comté (UBFC), Inserm, EFS BFC, UMR1098, Team « immunoregulation, immunopathology », RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France.,Department of Internal Medicine, Dijon University Hospital, Dijon, France
| | - Hélène Greigert
- Université Bourgogne Franche-Comté (UBFC), Inserm, EFS BFC, UMR1098, Team « immunoregulation, immunopathology », RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France
| | - Claire Tinel
- Université Bourgogne Franche-Comté (UBFC), Inserm, EFS BFC, UMR1098, Team « immunoregulation, immunopathology », RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France
| | - Olivier Adotevi
- UBFC, Inserm, EFS BFC, UMR1098, RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Philippe Saas
- UBFC, Inserm, EFS BFC, UMR1098, RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Maxime Samson
- Université Bourgogne Franche-Comté (UBFC), Inserm, EFS BFC, UMR1098, Team « immunoregulation, immunopathology », RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France.,Department of Internal Medicine, Dijon University Hospital, Dijon, France
| | - Sylvain Audia
- Université Bourgogne Franche-Comté (UBFC), Inserm, EFS BFC, UMR1098, Team « immunoregulation, immunopathology », RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France.,Department of Internal Medicine, Dijon University Hospital, Dijon, France
| | - Bernard Bonnotte
- Université Bourgogne Franche-Comté (UBFC), Inserm, EFS BFC, UMR1098, Team « immunoregulation, immunopathology », RIGHT Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France.,Department of Internal Medicine, Dijon University Hospital, Dijon, France
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Jean N, Perié L, Dumont E, Bertheau L, Balliau T, Caruana AMN, Amzil Z, Laabir M, Masseret E. Metal stresses modify soluble proteomes and toxin profiles in two Mediterranean strains of the distributed dinoflagellate Alexandrium pacificum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151680. [PMID: 34793790 DOI: 10.1016/j.scitotenv.2021.151680] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/25/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
HABs involving Alexandrium pacificum have been reported in metal-contaminated ecosystems, suggesting that this distributed species adapts to and/or can tolerate the effects of metals. Modifications in soluble proteomes and PST contents were characterized in two Mediterranean A. pacificum strains exposed to mono- or polymetallic stresses (zinc, lead, copper, cadmium). These strains were isolated from two anthropized locations: Santa Giusta Lagoon (Italy, SG C10-3) and the Tarragona seaport (Spain, TAR C5-4F). In both strains, metals primarily downregulated key photosynthesis proteins. Metals also upregulated other proteins involved in photosynthesis (PCP in both strains), the oxidative stress response (HSP 60, proteasome and SOD in SG C10-3; HSP 70 in TAR C5-4F), energy metabolism (AdK in TAR C5-4F), neoglucogenesis/glycolysis (GAPDH and PEP synthase in SG C10-3) and protein modification (PP in TAR C5-4F). These proteins, possibly involved in adaptive proteomic responses, may explain the development of these A. pacificum strains in metal-contaminated ecosystems. The two strains showed different proteomic responses to metals, with SG C10-3 upregulating more proteins, particularly PCP. Among the PSTs, regardless of the metal and the strain studied, C2 and GTX4 predominated, followed by GTX5. Under the polymetallic cocktail, (i) total PSTs, C2 and GTX4 reached the highest levels in SG C10-3 only, and (ii) total PSTs, C2, GTX5 and neoSTX were higher in SG C10-3 than in TAR C5-4F, whereas in SG C10-3 under copper stress, total PSTs, GTX5, GTX1 and C1 were higher than in the controls, revealing variability in PST biosynthesis between the two strains. Total PSTs, C2, GTX4 and GTX1 showed significant positive correlations with PCP, indicating that PST production may be positively related to photosynthesis. Our results showed that the A. pacificum strains adapt their proteomic and physiological responses to metals, which may contribute to their ecological success in highly anthropized areas.
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Affiliation(s)
- Natacha Jean
- Université de Toulon, Aix Marseille Univ, CNRS, IRD, MIO, Toulon, France.
| | - Luce Perié
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, New York University, 30(th) St., New York, NY 10016, USA
| | - Estelle Dumont
- UMR_MD1, Aix-Marseille Univ, U-1261-INSERM, SSA, IRBA, MCT, Marseille, France
| | - Lucie Bertheau
- UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté, AgroSup Dijon, esplanade Erasme, 21 000 Dijon, France
| | - Thierry Balliau
- PAPPSO-GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91 190 Gif-sur-Yvette, France
| | - Amandine M N Caruana
- IFREMER, Phycotoxin Laboratory, rue de l'île d'Yeu, BP 21105, 44 311 Nantes, France
| | - Zouher Amzil
- IFREMER, Phycotoxin Laboratory, rue de l'île d'Yeu, BP 21105, 44 311 Nantes, France
| | - Mohamed Laabir
- Marbec, Univ Montpellier, IRD, Ifremer, CNRS, Montpellier, France
| | - Estelle Masseret
- Marbec, Univ Montpellier, IRD, Ifremer, CNRS, Montpellier, France
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44
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Henry C, Bassignani A, Berland M, Langella O, Sokol H, Juste C. Modern Metaproteomics: A Unique Tool to Characterize the Active Microbiome in Health and Diseases, and Pave the Road towards New Biomarkers—Example of Crohn’s Disease and Ulcerative Colitis Flare-Ups. Cells 2022; 11:cells11081340. [PMID: 35456018 PMCID: PMC9028112 DOI: 10.3390/cells11081340] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 11/16/2022] Open
Abstract
Thanks to the latest developments in mass spectrometry, software and standards, metaproteomics is emerging as the vital complement of metagenomics, to make headway in understanding the actual functioning of living and active microbial communities. Modern metaproteomics offers new possibilities in the area of clinical diagnosis. This is illustrated here, for the still highly challenging diagnosis of intestinal bowel diseases (IBDs). Using bottom-up proteomics, we analyzed the gut metaproteomes of the same twenty faecal specimens processed either fresh or after a two-month freezing period. We focused on metaproteomes of microbial cell envelopes since it is an outstanding way of capturing host and host–microbe interaction signals. The protein profiles of pairs of fresh and frozen-thawed samples were closely related, making feasible deferred analysis in a distant diagnosis centre. The taxonomic and functional landscape of microbes in diverse IBD phenotypes—active ulcerative colitis, or active Crohn’s disease either with ileo-colonic or exclusive colonic localization—differed from each other and from the controls. Based on their specific peptides, we could identify proteins that were either strictly overrepresented or underrepresented in all samples of one clinical group compared to all samples of another group, paving the road for promising additional diagnostic tool for IBDs.
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Affiliation(s)
- Céline Henry
- PAPPSO, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.H.); (A.B.)
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
| | - Ariane Bassignani
- PAPPSO, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.H.); (A.B.)
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
- MGP, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
| | - Magali Berland
- MGP, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
| | - Olivier Langella
- PAPPSO, GQE-Le Moulon, AgroParisTech, CNRS, INRAE, Université Paris-Saclay, 91190 Gif-sur-Yvette, France;
| | - Harry Sokol
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
- Gastroenterology Department, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Sorbonne Université, 75012 Paris, France
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, Service de Gastro-Entérologie et Nutrition, Hôpital Saint-Antoine, Direction de la Recherche Clinique et de l’Innovation (DRCI) de l’AP-HP, CEDEX 12, 75571 Paris, France
| | - Catherine Juste
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
- Correspondence: ; Tel.: +33-67-72-82-035
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45
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Jan G, Tarnaud F, Rosa do Carmo FL, Illikoud N, Canon F, Jardin J, Briard-Bion V, Guyomarc'h F, Gagnaire V. The stressing life of Lactobacillus delbrueckii subsp. bulgaricus in soy milk. Food Microbiol 2022; 106:104042. [DOI: 10.1016/j.fm.2022.104042] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/04/2022] [Accepted: 04/19/2022] [Indexed: 12/23/2022]
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46
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Multiplex Detection of 24 Staphylococcal Enterotoxins in Culture Supernatant Using Liquid Chromatography Coupled to High-Resolution Mass Spectrometry. Toxins (Basel) 2022; 14:toxins14040249. [PMID: 35448858 PMCID: PMC9031063 DOI: 10.3390/toxins14040249] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 02/04/2023] Open
Abstract
Staphylococcal food poisoning outbreaks are caused by the ingestion of food contaminated with staphylococcal enterotoxins (SEs). Among the 27 SEs described in the literature to date, only a few can be detected using immuno-enzymatic-based methods that are strongly dependent on the availability of antibodies. Liquid chromatography, coupled to high-resolution mass spectrometry (LC-HRMS), has, therefore, been put forward as a relevant complementary method, but only for the detection of a limited number of enterotoxins. In this work, LC-HRMS was developed for the detection and quantification of 24 SEs. A database of 93 specific signature peptides and LC-HRMS parameters was optimized using sequences from 24 SEs, including their 162 variants. A label-free quantification protocol was established to overcome the absence of calibration standards. The LC-HRMS method showed high performance in terms of specificity, sensitivity, and accuracy when applied to 49 enterotoxin-producing strains. SE concentrations measured depended on both SE type and the coagulase-positive staphylococci (CPS) strain. This study indicates that LC-MS is a relevant alternative and complementary tool to ELISA methods. The advantages of LC-MS clearly lie in both the multiplex analysis of a large number of SEs, and the automated analysis of a high number of samples.
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47
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Zang L, Tarkowski ŁP, Morère-Le Paven MC, Zivy M, Balliau T, Clochard T, Bahut M, Balzergue S, Pelletier S, Landès C, Limami AM, Montrichard F. The Nitrate Transporter MtNPF6.8 Is a Master Sensor of Nitrate Signal in the Primary Root Tip of Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2022; 13:832246. [PMID: 35371178 PMCID: PMC8971838 DOI: 10.3389/fpls.2022.832246] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/22/2022] [Indexed: 06/12/2023]
Abstract
Nitrate is not only an essential nutrient for plants, but also a signal involved in plant development. We have previously shown in the model legume Medicago truncatula, that the nitrate signal, which restricts primary root growth, is mediated by MtNPF6.8, a nitrate transporter. Nitrate signal also induces changes in reactive oxygen species accumulation in the root tip due to changes in cell wall peroxidase (PODs) activity. Thus, it was interesting to determine the importance of the role of MtNPF6.8 in the regulation of the root growth by nitrate and identify the POD isoforms responsible for the changes in POD activity. For this purpose, we compared in M. truncatula a npf6.8 mutant and nitrate insensitive line deficient in MtNPF6.8 and the corresponding wild and sensitive genotype for their transcriptomic and proteomic responses to nitrate. Interestingly, only 13 transcripts and no protein were differently accumulated in the primary root tip of the npf6.8-3 mutant line in response to nitrate. The sensitivity of the primary root tip to nitrate appeared therefore to be strongly linked to the integrity of MtNPF6.8 which acts as a master mediator of the nitrate signal involved in the control of the root system architecture. In parallel, 7,259 and 493 genes responded, respectively, at the level of transcripts or proteins in the wild type, 196 genes being identified by both their transcript and protein. By focusing on these 196 genes, a concordance of expression was observed for most of them with 143 genes being up-regulated and 51 being down-regulated at the two gene expression levels. Their ontology analysis uncovered a high enrichment in POD genes, allowing the identification of POD candidates involved in the changes in POD activity previously observed in response to nitrate.
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Affiliation(s)
- Lili Zang
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
| | | | | | - Michel Zivy
- PAPPSO, GQE – Le Moulon, INRA, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Thierry Balliau
- PAPPSO, GQE – Le Moulon, INRA, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Thibault Clochard
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
| | | | - Sandrine Balzergue
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
| | - Sandra Pelletier
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
| | - Claudine Landès
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
| | - Anis M. Limami
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
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48
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Schallert K, Verschaffelt P, Mesuere B, Benndorf D, Martens L, Van Den Bossche T. Pout2Prot: An Efficient Tool to Create Protein (Sub)groups from Percolator Output Files. J Proteome Res 2022; 21:1175-1180. [PMID: 35143215 DOI: 10.1021/acs.jproteome.1c00685] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In metaproteomics, the study of the collective proteome of microbial communities, the protein inference problem is more challenging than in single-species proteomics. Indeed, a peptide sequence can be present not only in multiple proteins or protein isoforms of the same species, but also in homologous proteins from closely related species. To assign the taxonomy and functions of the microbial species, specialized tools have been developed, such as Prophane. This tool, however, is not directly compatible with post-processing tools such as Percolator. In this manuscript we therefore present Pout2Prot, which takes Percolator Output (.pout) files from multiple experiments and creates protein group and protein subgroup output files (.tsv) that can be used directly with Prophane. We investigated different grouping strategies and compared existing protein grouping tools to develop an advanced protein grouping algorithm that offers a variety of different approaches, allows grouping for multiple files, and uses a weighted spectral count for protein (sub)groups to reflect abundance. Pout2Prot is available as a web application at https://pout2prot.ugent.be and is installable via pip as a standalone command line tool and reusable software library. All code is open source under the Apache License 2.0 and is available at https://github.com/compomics/pout2prot.
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Affiliation(s)
- Kay Schallert
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, 39104 Magdeburg, Germany.,Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39104 Magdeburg, Germany
| | - Pieter Verschaffelt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium.,VIB - UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
| | - Bart Mesuere
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium.,VIB - UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
| | - Dirk Benndorf
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, 39104 Magdeburg, Germany.,Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39104 Magdeburg, Germany.,Microbiology, Department of Applied Biosciences and Process Technology, Anhalt University of Applied Sciences, 06366 Köthen, Germany
| | - Lennart Martens
- VIB - UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Tim Van Den Bossche
- VIB - UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
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49
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Simulated dynamic digestion reveals different peptide releases from human milk processed by means of holder or high temperature-short time pasteurization. Food Chem 2022; 369:130998. [PMID: 34507088 DOI: 10.1016/j.foodchem.2021.130998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/25/2021] [Accepted: 08/29/2021] [Indexed: 11/20/2022]
Abstract
High Temperature-Short Time (HTST) pasteurization was proposed as an alternative to Holder pasteurization (HOP) to increase the retention of specific human milk (HM) bioactive proteins. The present study explored whether HTST and HOP differently affect peptide release during simulated preterm infant gastrointestinal digestion. Raw (RHM), HOP- and HTST- pasteurized HM were digested using an in vitro dynamic system, and the identified peptides were analyzed by mass spectrometry and multivariate statistics. Before digestion, 158 peptides were identified in either RHM, HTST- or HOP- HM, mostly (84.4%) originating from β-casein (CASB). During gastric digestion, HOP-HM presented a greater number and more abundant specific CASB peptides. A delayed release of peptides was observed in RHM during the intestinal phase, with respect to both pasteurized HM. Although limited to gastric digestion, the HM peptidomic profile differed according to the pasteurization type, and the pattern of the HTST peptides showed a greater similarity with RHM.
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50
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Canon F, Briard-Bion V, Jardin J, Thierry A, Gagnaire V. Positive Interactions Between Lactic Acid Bacteria Could Be Mediated by Peptides Containing Branched-Chain Amino Acids. Front Microbiol 2022; 12:793136. [PMID: 35087496 PMCID: PMC8789265 DOI: 10.3389/fmicb.2021.793136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/20/2021] [Indexed: 11/22/2022] Open
Abstract
Lactic acid bacteria (LAB) are responsible for the sanitary, organoleptic, and health properties of most fermented products. Positive interactions between pairs of LAB strains, based on nitrogen dependencies, were previously demonstrated. In a chemically defined medium, using milk and lupin proteins as sole nitrogen source, two proteolytic strains were able to sustain the growth of non-proteolytic strains, but one did not. The objective of the present study was, thus, to determine which specific peptides were implicated in the positive interactions observed. Peptides produced and involved in the bacterial interactions were quantified using tandem mass spectrometry (LC-MS/MS). About 2,000 different oligopeptides ranging from 6 to more than 50 amino acids in length were identified during the time-course of the experiment. We performed a clustering approach to decipher the differences in peptide production during fermentation by the three proteolytic strains tested. We also performed sequence alignments on parental proteins and identified the cleavage site profiles of the three bacterial strains. Then, we characterized the peptides that were used by the non-proteolytic strains in monocultures. Hydrophobic and branched-chain amino acids within peptides were identified as essential in the interactions. Ultimately, better understanding how LAB can positively interact could be useful in multiple food-related fields, e.g., production of fermented food products with enhanced functional properties, or fermentation of new food matrices.
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Affiliation(s)
- Fanny Canon
- UMR STLO, INRAE, Institut Agro, Rennes, France
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