1
|
Hueber A, Kulyk H, Damont A, Nicol E, Alves S, Liuu S, Green M, Bertrand-Michel J, Cenac N, Fenaille F, Tabet JC. Energy Resolved Mass Spectrometry for Interoperable Non-resonant Collisional Spectra in Metabolomics. J Am Soc Mass Spectrom 2024; 35:834-838. [PMID: 38557041 DOI: 10.1021/jasms.3c00410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
In untargeted metabolomics, the unambiguous identification of metabolites remains a major challenge. This requires high-quality spectral libraries for reliable metabolite identification, which is essential for translating metabolomics data into meaningful biological information. Several attempts have been made to generate reproducible product ion spectra (PIS) under a low collision energy (ELab) regime and nonresonant collisional conditions but have not fully succeeded. We examined the ERMS (energy-resolved mass spectrometry) breakdown curves of two lipo-amino acids and showed the possibility to highlight "singular points", called descriptors hereafter (linked to respective ELab depending on the instrument), for each of the monomodal product ion profiles. Using several instruments based on different technologies, the PIS recorded at these specific ELab sites shows remarkable similarities. The descriptors appeared as being independent of the fragmentation mechanisms and can be used to overcome the main instrumental effects that limit the interoperability of spectral libraries. This proof-of-concept study, performed on two particular lipo-amino acids, demonstrates the high potential of ERMS-derived information to determine the instrument-specific ELab at which PIS recorded in nonresonant conditions become highly similar and instrument-independent, thus comparable across platforms. This innovative but straightforward approach could help remove some of the obstacles to metabolite identification in nontargeted metabolomics, putting an end to a challenging chimera.
Collapse
Affiliation(s)
- Amandine Hueber
- I2MC, Inserm, 31432 Toulouse, France
- IRSD, Université de Toulouse, INSERM, INRAE, INPENVT, 31024 Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31400 Toulouse, France
| | - Hanna Kulyk
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31400 Toulouse, France
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Annelaure Damont
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, MetaboHUB, 91191 Gif-sur-Yvette, France
| | - Edith Nicol
- Laboratoire de Chimie Moléculaire (LCM), CNRS, École Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Sandra Alves
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), 75005 Paris, France
| | - Sophie Liuu
- Food Safety Laboratory, ANSES, 94701 Maisons-Alfort, France
| | - Martin Green
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom
| | - Justine Bertrand-Michel
- I2MC, Inserm, 31432 Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31400 Toulouse, France
| | - Nicolas Cenac
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31400 Toulouse, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, MetaboHUB, 91191 Gif-sur-Yvette, France
| | - Jean-Claude Tabet
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, MetaboHUB, 91191 Gif-sur-Yvette, France
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), 75005 Paris, France
| |
Collapse
|
2
|
Liuu S, Nepelska M, Pfister H, Gamelas Magalhaes J, Chevalier G, Strozzi F, Billerey C, Maresca M, Nicoletti C, Di Pasquale E, Pechard C, Bardouillet L, Girardin SE, Boneca IG, Doré J, Blottière HM, Bonny C, Chene L, Cultrone A. Identification of a muropeptide precursor transporter from gut microbiota and its role in preventing intestinal inflammation. Proc Natl Acad Sci U S A 2023; 120:e2306863120. [PMID: 38127978 PMCID: PMC10756304 DOI: 10.1073/pnas.2306863120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/31/2023] [Indexed: 12/23/2023] Open
Abstract
The gut microbiota is a considerable source of biologically active compounds that can promote intestinal homeostasis and improve immune responses. Here, we used large expression libraries of cloned metagenomic DNA to identify compounds able to sustain an anti-inflammatory reaction on host cells. Starting with a screen for NF-κB activation, we have identified overlapping clones harbouring a heterodimeric ATP-binding cassette (ABC)-transporter from a Firmicutes. Extensive purification of the clone's supernatant demonstrates that the ABC-transporter allows for the efficient extracellular accumulation of three muropeptide precursor, with anti-inflammatory properties. They induce IL-10 secretion from human monocyte-derived dendritic cells and proved effective in reducing AIEC LF82 epithelial damage and IL-8 secretion in human intestinal resections. In addition, treatment with supernatants containing the muropeptide precursor reduces body weight loss and improves histological parameters in Dextran Sulfate Sodium (DSS)-treated mice. Until now, the source of peptidoglycan fragments was shown to come from the natural turnover of the peptidoglycan layer by endogenous peptidoglycan hydrolases. This is a report showing an ABC-transporter as a natural source of secreted muropeptide precursor and as an indirect player in epithelial barrier strengthening. The mechanism described here might represent an important component of the host immune homeostasis.
Collapse
Affiliation(s)
| | - Malgorzata Nepelska
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Food Microbial Ecology lab (Micalis), Université Paris-Saclay, Jouy-en-Josas78350, France
| | | | | | | | | | | | - Marc Maresca
- CNRS, Centrale Marseille, Institut des Sciences Moléculaires (iSm2) UMR7313, Aix Marseille Université, Marseille13013, France
| | - Cendrine Nicoletti
- CNRS, Centrale Marseille, Institut des Sciences Moléculaires (iSm2) UMR7313, Aix Marseille Université, Marseille13013, France
| | - Eric Di Pasquale
- Institut de NeuroPhysioPathologie (INP), Aix Marseille Université, UMR 7051, Marseille13005, France
| | | | | | - Stephen E. Girardin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ivo Gomperts Boneca
- Institut Pasteur, Université Paris Cité, CNRS Unité Mixe de Recherche 6047, INSERM U1306, Unité de Biologie et génétique de la paroi bactérienne, Paris75015, France
| | - Joel Doré
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Food Microbial Ecology lab (Micalis), Université Paris-Saclay, Jouy-en-Josas78350, France
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MetaGenoPolis, Université Paris-Saclay, Jouy-en-Josas78350, France
| | - Hervé M. Blottière
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Food Microbial Ecology lab (Micalis), Université Paris-Saclay, Jouy-en-Josas78350, France
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MetaGenoPolis, Université Paris-Saclay, Jouy-en-Josas78350, France
| | | | | | | |
Collapse
|
3
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| | | | | |
Collapse
|
4
|
Phung DK, Etienne C, Batista M, Langendijk-Genevaux P, Moalic Y, Laurent S, Liuu S, Morales V, Jebbar M, Fichant G, Bouvier M, Flament D, Clouet-d’Orval B. RNA processing machineries in Archaea: the 5'-3' exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3'-5' exoribonucleolytic RNA exosome machinery. Nucleic Acids Res 2020; 48:3832-3847. [PMID: 32030412 PMCID: PMC7144898 DOI: 10.1093/nar/gkaa052] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/14/2020] [Accepted: 01/23/2020] [Indexed: 01/22/2023] Open
Abstract
A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism.
Collapse
Affiliation(s)
- Duy Khanh Phung
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Clarisse Etienne
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Manon Batista
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Petra Langendijk-Genevaux
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Yann Moalic
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Sébastien Laurent
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Sophie Liuu
- Micalis Institute, PAPPSO, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Violette Morales
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Mohamed Jebbar
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Marie Bouvier
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Didier Flament
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, 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, F-31062 Toulouse, France
- To whom correspondence should be addressed. Tel: +33 561 335 875; Fax: +33 561 335 886;
| |
Collapse
|
5
|
Galdiero F, Bello AM, Spina A, Capiluongo A, Liuu S, De Marco M, Rosati A, Capunzo M, Napolitano M, Vuttariello E, Monaco M, Califano D, Turco MC, Chiappetta G, Vinh J, Chiappetta G. Identification of BAG3 target proteins in anaplastic thyroid cancer cells by proteomic analysis. Oncotarget 2018; 9:8016-8026. [PMID: 29487711 PMCID: PMC5814278 DOI: 10.18632/oncotarget.23858] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/30/2017] [Indexed: 11/25/2022] Open
Abstract
BAG3 protein is an apoptosis inhibitor and is highly expressed in Anaplastic Thyroid Cancer. We investigated the entire set of proteins modulated by BAG3 silencing in the human anaplastic thyroid 8505C cancer cells by using the Stable-Isotope Labeling by Amino acids in Cell culture strategy combined with mass spectrometry analysis. By this approach we identified 37 up-regulated and 54 down-regulated proteins in BAG3-silenced cells. Many of these proteins are reportedly involved in tumor progression, invasiveness and resistance to therapies. We focused our attention on an oncogenic protein, CAV1, and a tumor suppressor protein, SERPINB2, that had not previously been reported to be modulated by BAG3. Their expression levels in BAG3-silenced cells were confirmed by qRT-PCR and western blot analyses, disclosing two novel targets of BAG3 pro-tumor activity. We also examined the dataset of proteins obtained by the quantitative proteomics analysis using two tools, Downstream Effect Analysis and Upstream Regulator Analysis of the Ingenuity Pathways Analysis software. Our analyses confirm the association of the proteome profile observed in BAG3-silenced cells with an increase in cell survival and a decrease in cell proliferation and invasion, and highlight the possible involvement of four tumor suppressor miRNAs and TP53/63 proteins in BAG3 activity.
Collapse
Affiliation(s)
- Francesca Galdiero
- Functional Genomic Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Napoli, Italia
| | - Anna Maria Bello
- Functional Genomic Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Napoli, Italia
| | - Anna Spina
- Functional Genomic Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Napoli, Italia
| | - Anna Capiluongo
- Functional Genomic Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Napoli, Italia
| | - Sophie Liuu
- ESPCI ParisTech, Spectrométrie de Masse Biologique et Protéomique (SMBP), USR3149 CNRS, Paris, France
| | | | - Alessandra Rosati
- Biouniversa s.r.l., University of Salerno, Fisciano, Italy.,Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi (SA), Italy
| | - Mario Capunzo
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi (SA), Italy
| | - Maria Napolitano
- Functional Genomic Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Napoli, Italia
| | - Emilia Vuttariello
- Functional Genomic Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Napoli, Italia
| | - Mario Monaco
- Functional Genomic Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Napoli, Italia
| | - Daniela Califano
- Functional Genomic Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Napoli, Italia
| | - Maria Caterina Turco
- Biouniversa s.r.l., University of Salerno, Fisciano, Italy.,Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi (SA), Italy.,"SS. Giovanni di Dio e Ruggi d'Aragona-Schola Medica Salernitana", University of Salerno Hospital, Salerno, Italy
| | - Gennaro Chiappetta
- Functional Genomic Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Napoli, Italia
| | - Joëlle Vinh
- ESPCI ParisTech, Spectrométrie de Masse Biologique et Protéomique (SMBP), USR3149 CNRS, Paris, France
| | - Giovanni Chiappetta
- ESPCI ParisTech, Spectrométrie de Masse Biologique et Protéomique (SMBP), USR3149 CNRS, Paris, France
| |
Collapse
|
6
|
Fukuyama H, Ndiaye S, Hoffmann J, Rossier J, Liuu S, Vinh J, Verdier Y. On-bead tryptic proteolysis: an attractive procedure for LC-MS/MS analysis of the Drosophila caspase 8 protein complex during immune response against bacteria. J Proteomics 2012; 75:4610-9. [PMID: 22450469 DOI: 10.1016/j.jprot.2012.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 01/24/2012] [Accepted: 03/05/2012] [Indexed: 10/28/2022]
Abstract
This study aims to characterize the immune response against bacteria in Drosophila melanogaster. Obtaining a description of the in vivo state of protein complexes requires their isolation as a snapshot of physiological conditions before their identification. Affinity purification with streptavidin-biotin system is widely used to address this issue. However, because of the extraordinary stability of the interaction between streptavidin and biotin, the release of biotin-labeled bait remains a challenge. We transfected Drosophila cells with a DNA construct encoding a biotin-tagged Dredd protein (ortholog of caspase 8). After affinity purification, different strategies were evaluated, and proteins analyzed by LC-MS/MS mass spectrometry. The on-bead digestion allowed the identification of more proteins associated to the Dredd complex than different protocols using competitive or acid elution. A functional assay showed that a large part of the proteins specifically identified in the Dredd sample are functionally involved in the activation of the Imd pathway. These proteins are immune response proteins (BG4, Q9VP57), stress response proteins (HSP7C, Q9VXQ5), structural proteins (TBB1, CP190), a protein biosynthesis protein (Q9W1B9) and an antioxidant system protein (SODC). Our results clearly show that on-bead digestion of proteins is an attractive procedure for the study of protein complexes by mass spectrometry. This article is part of a Special Issue entitled: Translational Proteomics.
Collapse
Affiliation(s)
- Hidehiro Fukuyama
- Centre National de La Recherche Scientifique, UPR9022, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg, France
| | | | | | | | | | | | | |
Collapse
|