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Pees B, Peters L, Treitz C, Hamerich IK, Kissoyan KAB, Tholey A, Dierking K. The Caenorhabditis elegans proteome response to two protective Pseudomonas symbionts. mBio 2024; 15:e0346323. [PMID: 38411078 PMCID: PMC11005407 DOI: 10.1128/mbio.03463-23] [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: 01/04/2024] [Accepted: 02/05/2024] [Indexed: 02/28/2024] Open
Abstract
The Caenorhabditis elegans natural microbiota isolates Pseudomonas lurida MYb11 and Pseudomonas fluorescens MYb115 protect the host against pathogens through distinct mechanisms. While P. lurida produces an antimicrobial compound and directly inhibits pathogen growth, P. fluorescens MYb115 protects the host without affecting pathogen growth. It is unknown how these two protective microbes affect host biological processes. We used a proteomics approach to elucidate the C. elegans response to MYb11 and MYb115. We found that both Pseudomonas isolates increase vitellogenin protein production in young adults, which confirms previous findings on the effect of microbiota on C. elegans reproductive timing. Moreover, the C. elegans responses to MYb11 and MYb115 exhibit common signatures with the response to other vitamin B12-producing bacteria, emphasizing the importance of vitamin B12 in C. elegans-microbe metabolic interactions. We further analyzed signatures in the C. elegans response specific to MYb11 or MYb115. We provide evidence for distinct modifications in lipid metabolism by both symbiotic microbes. We could identify the activation of host-pathogen defense responses as an MYb11-specific proteome signature and provide evidence that the intermediate filament protein IFB-2 is required for MYb115-mediated protection. These results indicate that MYb11 not only produces an antimicrobial compound but also activates host antimicrobial defenses, which together might increase resistance to infection. In contrast, MYb115 affects host processes such as lipid metabolism and cytoskeleton dynamics, which might increase host tolerance to infection. Overall, this study pinpoints proteins of interest that form the basis for additional exploration into the mechanisms underlying C. elegans microbiota-mediated protection from pathogen infection and other microbiota-mediated traits.IMPORTANCESymbiotic bacteria can defend their host against pathogen infection. While some protective symbionts directly interact with pathogenic bacteria, other protective symbionts elicit a response in the host that improves its own pathogen defenses. To better understand how a host responds to protective symbionts, we examined which host proteins are affected by two protective Pseudomonas bacteria in the model nematode Caenorhabditis elegans. We found that the C. elegans response to its protective symbionts is manifold, which was reflected in changes in proteins that are involved in metabolism, the immune system, and cell structure. This study provides a foundation for exploring the contribution of the host response to symbiont-mediated protection from pathogen infection.
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Affiliation(s)
- Barbara Pees
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrecht University, Kiel, Germany
| | - Lena Peters
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrecht University, Kiel, Germany
| | - Christian Treitz
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrecht University, Kiel, Germany
| | - Inga K. Hamerich
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrecht University, Kiel, Germany
| | - Kohar A. B. Kissoyan
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrecht University, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrecht University, Kiel, Germany
| | - Katja Dierking
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrecht University, Kiel, Germany
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Treitz C, Müller-Marienburg N, Meliß RR, Urban P, Axmann HD, Siebert F, Becker K, Martens K, Behrens HM, Gericke E, Tholey A, Röcken C. ATTR- and AFib amyloid - two different types of amyloid in the annular ligament of trigger finger. Amyloid 2023; 30:394-406. [PMID: 37353960 DOI: 10.1080/13506129.2023.2226298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 06/12/2023] [Indexed: 06/25/2023]
Abstract
INTRODUCTION Histological examination of tissue specimens obtained during surgical treatment of trigger finger frequently encountered unclassifiable amyloid deposits in the annular ligament. We systematically explored this unknown type by a comprehensive analysis using histology, immunohistochemistry, and quantitative mass spectrometry-based proteomics. METHODS 205 tissue specimens of annular ligaments were obtained from 172 patients. Each specimen was studied by histology and immunohistochemistry. Tissue specimens obtained from ten patients with histology proven amyloid in annular ligament were analysed by label-free quantitative proteomics. Histological and immunohistochemical findings were correlated with patient demographics. RESULTS Amyloid was present as band like deposits along the surface of annular ligament, dot like or patchy deposits within the matrix. Immunohistochemistry identified ATTR amyloid in 92 specimens (mostly patchy in the matrix), while the band like deposits of 100 specimens remained unclassifiable. Proteomic profiles identified the unknown amyloid as most likely of fibrinogen origin. The complete cohort was re-examined by immunohistochemistry using a custom-made antibody and confirmed the presence of fibrinogen alpha-chain (FGA) in a hitherto unclassifiable type of amyloid in annular ligament. CONCLUSION Our study shows that two different types of amyloid affect the annular ligament, ATTR amyloid and AFib amyloid, with distinct demographic patient characteristics and histomorphological deposition patterns.
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Affiliation(s)
- Christian Treitz
- Systematic Proteome Research & Bioanalytics, Institute of Experimental Medicine, Christian-Albrechts-University, Kiel, Germany
| | | | | | - Peter Urban
- Institute of Pathology and Dermatopathology, Hannover, Germany
| | | | | | | | - Klaus Martens
- Clinics for Orthopedics and Hand-Surgery, Buchholz, Germany
| | | | - Eva Gericke
- Department of Pathology, Christian-Albrechts-University, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute of Experimental Medicine, Christian-Albrechts-University, Kiel, Germany
| | - Christoph Röcken
- Department of Pathology, Christian-Albrechts-University, Kiel, Germany
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Rueter J, Rimbach G, Treitz C, Schloesser A, Lüersen K, Tholey A, Huebbe P. The mitochondrial BCKD complex interacts with hepatic apolipoprotein E in cultured cells in vitro and mouse livers in vivo. Cell Mol Life Sci 2023; 80:59. [PMID: 36749362 PMCID: PMC9905200 DOI: 10.1007/s00018-023-04706-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/22/2022] [Accepted: 01/23/2023] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS Apolipoprotein E (APOE) is known for its role in lipid metabolism and its association with age-related disease pathology. The aim of the present work was to identify previously unknown functions of APOE based on the detection of novel APOE protein-protein interaction candidates. APPROACH AND RESULTS APOE targeted replacement mice and transfected cultured hepatocytes expressing the human isoforms APOE3 and APOE4 were used. For 7 months, APOE3 and APOE4 mice were fed a high-fat and high-sugar diet to induce obesity, while a subgroup was subjected to 30% dietary restriction. Proteomic analysis of coimmunoprecipitation products from APOE mouse liver extracts revealed 28 APOE-interacting candidate proteins, including branched-chain alpha-keto acid dehydrogenase (BCKD) complex subunit alpha (BCKDHA) and voltage-dependent anion-selective channel 1 (VDAC1). The binding of APOE and BCKDHA was verified in situ by proximity ligation assay in cultured cells. The activity of the BCKD enzyme complex was significantly higher in obese APOE4 mice than in APOE3 mice, while the plasma levels of branched-chain amino acids and mTOR signalling proteins were not different. However, the protein-protein interaction with VDAC1 was strongly induced in APOE3 and APOE4 mice upon dietary restriction, suggesting a prominent role of APOE in mitochondrial function. CONCLUSIONS The protein-protein interactions of APOE with BCKDHA and VDAC1 appear to be of physiological relevance and are modulated upon dietary restriction. Because these are mitochondrial proteins, it may be suggested that APOE is involved in mitochondria-related processes and adaptation to hepatic energy demands.
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Affiliation(s)
- Johanna Rueter
- Institute of Human Nutrition and Food Science, University of Kiel, Hermann-Rodewald-Strasse 6, 24118, Kiel, Germany
| | - Gerald Rimbach
- Institute of Human Nutrition and Food Science, University of Kiel, Hermann-Rodewald-Strasse 6, 24118, Kiel, Germany.
| | - Christian Treitz
- Institute of Experimental Medicine, University of Kiel, Niemannsweg 11, 24105, Kiel, Germany
| | - Anke Schloesser
- Institute of Human Nutrition and Food Science, University of Kiel, Hermann-Rodewald-Strasse 6, 24118, Kiel, Germany
| | - Kai Lüersen
- Institute of Human Nutrition and Food Science, University of Kiel, Hermann-Rodewald-Strasse 6, 24118, Kiel, Germany
| | - Andreas Tholey
- Institute of Experimental Medicine, University of Kiel, Niemannsweg 11, 24105, Kiel, Germany
| | - Patricia Huebbe
- Institute of Human Nutrition and Food Science, University of Kiel, Hermann-Rodewald-Strasse 6, 24118, Kiel, Germany
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Genth J, Kaleja P, Treitz C, Schäfer K, Graspeuntner S, Rupp J, Tholey A. The intracellular proteome of the gut bacterium Bacteroides thetaiotaomicron is widely unaffected by a switch from glucose to sucrose as main carbohydrate source. Proteomics 2022; 22:e2200189. [PMID: 35906788 DOI: 10.1002/pmic.202200189] [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: 05/09/2022] [Revised: 07/13/2022] [Accepted: 07/25/2022] [Indexed: 12/29/2022]
Abstract
Bacteroides thetaiotaomicron is a gram negative bacterium within the human gut microbiome that metabolizes a wide range of dietary and mucosal polysaccharides. Here, we analyze the proteome response of B. thetaiotaomicron cultivated on two different carbon sources, glucose and sucrose. Two quantitative LC-MS based proteomics approaches, encompassing label free quantification and isobaric labeling by tandem mass tags were applied. The results obtained by both workflows were compared with respect to the number of identified and quantified proteins, peptides supporting identification and quantification, sequence coverage, and reproducibility. A total of 1719 and 1696 proteins, respectively, were quantified, covering 35 % of the predicted B. thetaiotaomicron proteome. The data show that B. thetaiotaomicron widely maintains its intracellular proteome upon change of the carbohydrates and that major changes are observed solely in the machinery necessary to make use of the carbon sources provided. With respect to the central role of carbohydrates on gut health these data contribute to the understanding of how different carbohydrates contribute to shape bacterial community in the gut microbiome. All proteomics raw data have been uploaded to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD033704.
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Affiliation(s)
- Jerome Genth
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Patrick Kaleja
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Christian Treitz
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Kathrin Schäfer
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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5
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Treitz C, Gottwald J, Gericke E, Urban P, Meliß RR, Axmann HD, Siebert F, Becker K, Tholey A, Röcken C. Quantitative proteome profiling provides evidence of an activation of the complement cascade in ATTR amyloidosis. Amyloid 2022; 29:102-109. [PMID: 34913770 DOI: 10.1080/13506129.2021.2015316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Amyloidosis is a disease group caused by pathological aggregation and deposition of peptides in diverse tissue sites. Apart from the fibril protein, amyloid deposits frequently enclose non-fibrillar constituents. In this study, carpal tunnel tissue sections with ATTR amyloid were analysed by quantitative mass spectrometry-based proteomics. Following manual dissection, tissue samples of equal size and with heterogeneous amyloid load were dissected and forwarded to bottom-up proteome analysis and label-free protein profiling. The amyloid-associated proteins showed significant correlations of label-free intensity profiles. A comprehensive list of 83 proteins specifically enriched in amyloid deposits was discovered. In addition to well-known signature proteins (e.g. apolipoprotein E, apolipoprotein A-IV, and vitronectin), 22 members of the complement system, including all seven components of the membrane attack complex could be associated to the disease. These data lend support to the hypothesis that the complement system is activated in ATTR amyloidosis.
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Affiliation(s)
- Christian Treitz
- Systematic Proteome Research and Bioanalytics, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Juliane Gottwald
- Department of Pathology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Eva Gericke
- Department of Pathology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Peter Urban
- Institute of Pathology and Dermatopathology, Hannover, Germany
| | | | | | | | | | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Christoph Röcken
- Department of Pathology, Christian-Albrechts-University Kiel, Kiel, Germany
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Kaulich PT, Winkels K, Kaulich TB, Treitz C, Cassidy L, Tholey A. MSTopDiff: A Tool for the Visualization of Mass Shifts in Deconvoluted Top-Down Proteomics Data for the Database-Independent Detection of Protein Modifications. J Proteome Res 2021; 21:20-29. [PMID: 34818005 DOI: 10.1021/acs.jproteome.1c00766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Top-down proteomics analyzes intact proteoforms with all of their post-translational modifications and genetic and RNA splice variants. In addition, modifications introduced either deliberately or inadvertently during sample preparation, that is, via oxidation, alkylation, or labeling reagents, or through the formation of noncovalent adducts (e.g., detergents) further increase the sample complexity. To facilitate the recognition of protein modifications introduced during top-down analysis, we developed MSTopDiff, a software tool with a graphical user interface written in Python, which allows one to detect protein modifications by calculating and visualizing mass differences in top-down data without the prerequisite of a database search. We demonstrate the successful application of MSTopDiff for the detection of artifacts originating from oxidation, formylation, overlabeling during isobaric labeling, and adduct formation with cations or sodium dodecyl sulfate. MSTopDiff offers several modes of data representation using deconvoluted MS1 or MS2 spectra. In addition to artificial modifications, the tool enables the visualization of biological modifications such as phosphorylation and acetylation. MSTopDiff provides an overview of the artificial and biological modifications in top-down proteomics samples, which makes it a valuable tool in quality control of standard workflows and for parameter evaluation during method development.
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Affiliation(s)
- Philipp T Kaulich
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Konrad Winkels
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Tobias B Kaulich
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Christian Treitz
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Liam Cassidy
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
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7
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Lipinski S, Pfeuffer S, Arnold P, Treitz C, Aden K, Ebsen H, Falk-Paulsen M, Gisch N, Fazio A, Kuiper J, Luzius A, Billmann-Born S, Schreiber S, Nuñez G, Beer HD, Strowig T, Lamkanfi M, Tholey A, Rosenstiel P. Prdx4 limits caspase-1 activation and restricts inflammasome-mediated signaling by extracellular vesicles. EMBO J 2019; 38:e101266. [PMID: 31544965 PMCID: PMC6792017 DOI: 10.15252/embj.2018101266] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 11/29/2018] [Revised: 08/05/2019] [Accepted: 08/21/2019] [Indexed: 12/15/2022] Open
Abstract
Inflammasomes are cytosolic protein complexes, which orchestrate the maturation of active IL‐1β by proteolytic cleavage via caspase‐1. Although many principles of inflammasome activation have been described, mechanisms that limit inflammasome‐dependent immune responses remain poorly defined. Here, we show that the thiol‐specific peroxidase peroxiredoxin‐4 (Prdx4) directly regulates IL‐1β generation by interfering with caspase‐1 activity. We demonstrate that caspase‐1 and Prdx4 form a redox‐sensitive regulatory complex via caspase‐1 cysteine 397 that leads to caspase‐1 sequestration and inactivation. Mice lacking Prdx4 show an increased susceptibility to LPS‐induced septic shock. This effect was phenocopied in mice carrying a conditional deletion of Prdx4 in the myeloid lineage (Prdx4‐ΔLysMCre). Strikingly, we demonstrate that Prdx4 co‐localizes with inflammasome components in extracellular vesicles (EVs) from inflammasome‐activated macrophages. Purified EVs are able to transmit a robust IL‐1β‐dependent inflammatory response in vitro and also in recipient mice in vivo. Loss of Prdx4 boosts the pro‐inflammatory potential of EVs. These findings identify Prdx4 as a critical regulator of inflammasome activity and provide new insights into remote cell‐to‐cell communication function of inflammasomes via macrophage‐derived EVs.
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Affiliation(s)
- Simone Lipinski
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Steffen Pfeuffer
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Philipp Arnold
- Anatomical Institute, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Christian Treitz
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-University, Kiel, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.,1st Department of Internal Medicine, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Henriette Ebsen
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Maren Falk-Paulsen
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Antonella Fazio
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Jan Kuiper
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Anne Luzius
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Susanne Billmann-Born
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Stefan Schreiber
- 1st Department of Internal Medicine, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Gabriel Nuñez
- Department of Pathology, School of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Hans-Dietmar Beer
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland.,Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mohamed Lamkanfi
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-University, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
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8
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Rabeharindranto H, Castaño-Cerezo S, Lautier T, Garcia-Alles LF, Treitz C, Tholey A, Truan G. Enzyme-fusion strategies for redirecting and improving carotenoid synthesis in S. cerevisiae. Metab Eng Commun 2019; 8:e00086. [PMID: 30723675 PMCID: PMC6350077 DOI: 10.1016/j.mec.2019.e00086] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 03/06/2018] [Revised: 12/20/2018] [Accepted: 01/11/2019] [Indexed: 12/22/2022] Open
Abstract
Spatial clustering of enzymes has proven an elegant approach to optimize metabolite transfer between enzymes in synthetic metabolic pathways. Among the multiple methods used to promote colocalisation, enzyme fusion is probably the simplest. Inspired by natural systems, we have explored the metabolic consequences of spatial reorganizations of the catalytic domains of Xanthophyllomyces dendrorhous carotenoid enzymes produced in Saccharomyces cerevisiae. Synthetic genes encoding bidomain enzymes composed of CrtI and CrtB domains from the natural CrtYB fusion were connected in the two possible orientations, using natural and synthetic linkers. A tridomain enzyme (CrtB, CrtI, CrtY) harboring the full β-carotene producing pathway was also constructed. Our results demonstrate that domain order and linker properties considerably impact both the expression and/or stability of the constructed proteins and the functionality of the catalytic domains, all concurring to either diminish or boost specific enzymatic steps of the metabolic pathway. Remarkably, the yield of β-carotene production doubled with the tridomain fusion while precursor accumulation decreased, leading to an improvement of the pathway efficiency, when compared to the natural system. Our data strengthen the idea that fusion of enzymatic domains is an appropriate technique not only to achieve spatial confinement and enhance the metabolic flux but also to produce molecules not easily attainable with natural enzymatic configurations, even with membrane bound enzymes.
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Affiliation(s)
| | | | - Thomas Lautier
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | | | - Christian Treitz
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Gilles Truan
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Correspondence to: LISBP, 135 Avenue de Rangueil, 31077 Toulouse Cedex 04, France.
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Cassidy L, Petersen C, Treitz C, Dierking K, Schulenburg H, Leippe M, Tholey A. The Caenorhabditis elegans Proteome Response to Naturally Associated Microbiome Members of the Genus Ochrobactrum. Proteomics 2018. [PMID: 29513928 DOI: 10.1002/pmic.201700426] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The nematode Caenorhabditis elegans interacts with a variety of bacteria as it feeds on microbes, and a number of these both associate and persist within the worm's intestine. Host-microbe interactions in C. elegans have been analyzed primarily at the transcriptome level with the host response often been monitored after challenge with pathogens. We assessed the proteome of C. elegans after growth on bacteria capable of colonizing its gut, via a comparative analysis of the nematode exposed to two naturally associated Ochrobactrum spp. (MYb71, MYb237) versus C. elegans grown on Escherichia coli OP50. A total of 4677 C. elegans proteins were identified, 3941 quantified. Significant alterations in protein abundances were observed for 122 proteins, 48 higher and 74 lower in abundance. We observed an increase in abundance of proteins potentially regulated via host signaling pathways, in addition to proteins involved in processing of foreign entities (e.g., lipase, proteases, glutathione metabolism). Decreased in abundance were proteins involved in both degradation and biosynthesis of amino acids, and enzymes associated with the degradation of peptidoglycan (lysozymes). The protein level differences between C. elegans grown on native microbiome members compared to the laboratory food bacterium may help to identify molecular processes involved in host-microbe interactions.
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Affiliation(s)
- Liam Cassidy
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Carola Petersen
- Zoological Institute, Comparative Immunobiology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Zoological Institute, Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Christian Treitz
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Katja Dierking
- Zoological Institute, Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Hinrich Schulenburg
- Zoological Institute, Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Matthias Leippe
- Zoological Institute, Comparative Immunobiology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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Leipert J, Treitz C, Leippe M, Tholey A. Identification and Quantification of N-Acyl Homoserine Lactones Involved in Bacterial Communication by Small-Scale Synthesis of Internal Standards and Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. J Am Soc Mass Spectrom 2017; 28:2538-2547. [PMID: 28856620 DOI: 10.1007/s13361-017-1777-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/01/2017] [Accepted: 08/01/2017] [Indexed: 06/07/2023]
Abstract
N-acyl homoserine lactones (AHL) are small signal molecules involved in the quorum sensing of many gram-negative bacteria, and play an important role in biofilm formation and pathogenesis. Present analytical methods for identification and quantification of AHL require time-consuming sample preparation steps and are hampered by the lack of appropriate standards. By aiming at a fast and straightforward method for AHL analytics, we investigated the applicability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Suitable MALDI matrices, including crystalline and ionic liquid matrices, were tested and the fragmentation of different AHL in collision-induced dissociation MS/MS was studied, providing information about characteristic marker fragments ions. Employing small-scale synthesis protocols, we established a versatile and cost-efficient procedure for fast generation of isotope-labeled AHL standards, which can be used without extensive purification and yielded accurate standard curves. Quantitative analysis was possible in the low pico-molar range, with lower limits of quantification reaching from 1 to 5 pmol for different AHL. The developed methodology was successfully applied in a quantitative MALDI MS analysis of low-volume culture supernatants of Pseudomonas aeruginosa. Graphical abstract ᅟ.
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Affiliation(s)
- Jan Leipert
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Christian Treitz
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Matthias Leippe
- Zoological Institute, Comparative Immunobiology, Christian-Albrechts-Universität zu Kiel, 24114, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany.
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Treitz C, Enjalbert B, Portais JC, Letisse F, Tholey A. Differential quantitative proteome analysis of Escherichia coli grown on acetate versus glucose. Proteomics 2016; 16:2742-2746. [PMID: 27604403 DOI: 10.1002/pmic.201600303] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 08/26/2016] [Accepted: 09/02/2016] [Indexed: 01/07/2023]
Abstract
Relative protein abundances of Escherichia coli MG1655 growing exponentially on minimal medium with acetate or glucose as the sole carbon source were investigated in a quantitative shotgun proteome analysis with TMT6-plex isobaric tags. Peptides were separated by high resolution high/low pH 2D-LC, using an optimized fraction pooling scheme followed by mass spectrometric analysis. Quantitative data were acquired for 2099 proteins covering 49% of the predicted E. coli proteins, showing system-wide effects of growth conditions. In total, 507 proteins showed a fold change of at least 1.5 and 205 proteins changed by more than twofold. Significant differences in abundance were observed for most of the proteins in the central carbon metabolism and in proteins relevant for amino acid and protein synthesis, processing of environmental information and scavenging of a variety of alternate carbon sources. Periplasmic-binding proteins were also more abundant on acetate, especially proteins involved in scavenging extracellular resources such as sugars. All MS data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (dataset identifier PXD003863).
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Affiliation(s)
- Christian Treitz
- Systematische Proteomforschung & Bioanalytik, Institut für Experimentelle Medizin, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Brice Enjalbert
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | | | - Fabien Letisse
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Andreas Tholey
- Systematische Proteomforschung & Bioanalytik, Institut für Experimentelle Medizin, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
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Wilde SC, Treitz C, Keppler JK, Koudelka T, Palani K, Tholey A, Rawel HM, Schwarz K. β-Lactoglobulin as nanotransporter – Part II: Characterization of the covalent protein modification by allicin and diallyl disulfide. Food Chem 2016; 197:1022-9. [DOI: 10.1016/j.foodchem.2015.11.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 10/10/2015] [Accepted: 11/03/2015] [Indexed: 10/22/2022]
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13
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Tholey A, Treitz C, Kussmann M, Bendixen E, Schrimpf SP, Hengartner MO. Model Organisms Proteomics-From Holobionts to Human Nutrition. Proteomics 2013; 13:2537-41. [DOI: 10.1002/pmic.201370144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Andreas Tholey
- Division of Systematic Proteome Research; Institute for Experimental Medicine; Christian-Albrechts-Universität zu Kiel; Kiel; Germany
| | - Christian Treitz
- Division of Systematic Proteome Research; Institute for Experimental Medicine; Christian-Albrechts-Universität zu Kiel; Kiel; Germany
| | | | - Emöke Bendixen
- Department of Molecular Biology and Genetics; Laboratory of Proteomics and Mass spectrometry; Aarhus University; Arhus; Denmark
| | - Sabine P. Schrimpf
- Institute of Molecular Life Sciences; University of Zurich; Zurich; Switzerland
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