1
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Wiese C, Abele M, Al B, Altmann M, Steiner A, Kalbfuß N, Strohmayr A, Ravikumar R, Park CH, Brunschweiger B, Meng C, Facher E, Ehrhardt DW, Falter-Braun P, Wang ZY, Ludwig C, Assaad FF. Regulation of adaptive growth decisions via phosphorylation of the TRAPPII complex in Arabidopsis. J Cell Biol 2024; 223:e202311125. [PMID: 38558238 PMCID: PMC10983811 DOI: 10.1083/jcb.202311125] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/31/2024] [Accepted: 02/15/2024] [Indexed: 04/04/2024] Open
Abstract
Plants often adapt to adverse or stress conditions via differential growth. The trans-Golgi network (TGN) has been implicated in stress responses, but it is not clear in what capacity it mediates adaptive growth decisions. In this study, we assess the role of the TGN in stress responses by exploring the previously identified interactome of the Transport Protein Particle II (TRAPPII) complex required for TGN structure and function. We identified physical and genetic interactions between AtTRAPPII and shaggy-like kinases (GSK3/AtSKs) and provided in vitro and in vivo evidence that the TRAPPII phosphostatus mediates adaptive responses to abiotic cues. AtSKs are multifunctional kinases that integrate a broad range of signals. Similarly, the AtTRAPPII interactome is vast and considerably enriched in signaling components. An AtSK-TRAPPII interaction would integrate all levels of cellular organization and instruct the TGN, a central and highly discriminate cellular hub, as to how to mobilize and allocate resources to optimize growth and survival under limiting or adverse conditions.
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Affiliation(s)
- Christian Wiese
- Biotechnology of Natural Products, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Miriam Abele
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Benjamin Al
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Melina Altmann
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Center Munich, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Alexander Steiner
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Nils Kalbfuß
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Alexander Strohmayr
- Biotechnology of Natural Products, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Raksha Ravikumar
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chan Ho Park
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Barbara Brunschweiger
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Eva Facher
- Systematic Botany and Mycology, Faculty of Biology, Ludwig-Maximilians-Universität (LMU) München, Planegg-Martinsried, Germany
| | - David W. Ehrhardt
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Pascal Falter-Braun
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Center Munich, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Farhah F. Assaad
- Biotechnology of Natural Products, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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2
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Khan MM, Sidorczuk K, Becker J, Aleksandrowicz A, Baraniewicz K, Ludwig C, Ali A, Kingsley RA, Schierack P, Kolenda R. Characterization of clumpy adhesion of Escherichia coli to human cells and associated factors influencing antibiotic sensitivity. Microbiol Spectr 2024; 12:e0260623. [PMID: 38530058 DOI: 10.1128/spectrum.02606-23] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 03/12/2024] [Indexed: 03/27/2024] Open
Abstract
Escherichia coli intestinal infection pathotypes are characterized by distinct adhesion patterns, including the recently described clumpy adhesion phenotype. Here, we identify and characterize the genetic factors contributing to the clumpy adhesion of E. coli strain 4972. In this strain, the transcriptome and proteome of adhered bacteria were found to be distinct from planktonic bacteria in the supernatant. A total of 622 genes in the transcriptome were differentially expressed in bacteria present in clumps relative to the planktonic bacteria. Seven genes targeted for disruption had variable distribution in different pathotypes and nonpathogenic E. coli, with the pilV and spnT genes being the least frequent or absent from most groups. Deletion (Δ) of five differentially expressed genes, flgH, ffp, pilV, spnT, and yggT, affected motility, adhesion, or antibiotic stress. ΔflgH exhibited 80% decrease and ΔyggT depicted 184% increase in adhesion, and upon complementation, adhesion was significantly reduced to 13%. ΔflgH lost motility and was regenerated when complemented, whereas Δffp had significantly increased motility, and reintroduction of the same gene reduced it to the wild-type level. The clumps produced by Δffp and ΔspnT were more resistant and protected the bacteria, with ΔspnT showing the best clump formation in terms of ampicillin stress protection. ΔyggT had the lowest tolerance to gentamicin, where the antibiotic stress completely eliminated the bacteria. Overall, we were able to investigate the influence of clump formation on cell surface adhesion and antimicrobial tolerance, with the contribution of several factors crucial to clump formation on susceptibility to the selected antibiotics. IMPORTANCE The study explores a biofilm-like clumpy adhesion phenotype in Escherichia coli, along with various factors and implications for antibiotic susceptibility. The phenotype permitted the bacteria to survive the onslaught of high antibiotic concentrations. Profiles of the transcriptome and proteome allowed the differentiation between adhered bacteria in clumps and planktonic bacteria in the supernatant. The deletion mutants of genes differentially expressed between adhered and planktonic bacteria, i.e., flgH, ffp, pilV, spnT, and yggT, and respective complementations in trans cemented their roles in multiple capacities. ffp, an uncharacterized gene, is involved in motility and resistance to ampicillin in a clumpy state. The work also affirms for the first time the role of the yggT gene in adhesion and its involvement in susceptibility against another aminoglycoside antibiotic, i.e., gentamicin. Overall, the study contributes to the mechanisms of biofilm-like adhesion phenotype and understanding of the antimicrobial therapy failures and infections of E. coli.
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Affiliation(s)
- Muhammad Moman Khan
- Institute for Biotechnology, Brandenburg University of Technology (BTU) Cottbus-Senftenberg, Senftenberg, Germany
| | - Katarzyna Sidorczuk
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Juliane Becker
- Institute for Biotechnology, Brandenburg University of Technology (BTU) Cottbus-Senftenberg, Senftenberg, Germany
| | - Adrianna Aleksandrowicz
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Karolina Baraniewicz
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wrocław, Wrocław, Poland
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences, Technical University Munich (TUM), Munich, Germany
| | - Aamir Ali
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Robert A Kingsley
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Peter Schierack
- Institute for Biotechnology, Brandenburg University of Technology (BTU) Cottbus-Senftenberg, Senftenberg, Germany
| | - Rafał Kolenda
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
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Liu Y, Angelov A, Übelacker M, Baudrexl M, Ludwig C, Rühmann B, Sieber V, Liebl W. Proteomic analysis of Viscozyme L and its major enzyme components for pectic substrate degradation. Int J Biol Macromol 2024; 266:131309. [PMID: 38580019 DOI: 10.1016/j.ijbiomac.2024.131309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/14/2024] [Accepted: 03/30/2024] [Indexed: 04/07/2024]
Abstract
Enzymatic degradation of plant biomass requires the coordinated action of various enzymes. In this study, the production of reducing sugars from pectic substrates and sugar beet pulp (SBP) was investigated and compared using commercial enzyme preparations, including M2, pectinase (E1), Viscozyme L (V-L) and L-40. V-L, a cellulolytic enzyme mix produced by Aspergillus sp. was further evaluated as the most robust enzyme cocktail with the strongest SBP degradation ability in terms of the release of monosaccharides, methanol, and acetate from SBP. Mass-spectrometry-based proteomics analysis of V-L revealed 156 individual proteins. Of these, 101 proteins were annotated as containing a carbohydrate-active enzyme module. Notably, of the 50 most abundant proteins, ca. 44 % were predicted to be involved in pectin degradation. To reveal the role of individual putative key enzymes in pectic substrate decomposition, two abundant galacturonases (PglA and PglB), were heterologously expressed in Pichia pastoris and further characterized. PglA and PglB demonstrated maximum activity at 57 °C and 68 °C, respectively, and exhibited endo-type cleavage patterns towards polygalacturonic acid. Further studies along this line may lead to a better understanding of efficient SBP degradation and may help to design improved artificial enzyme mixtures with lower complexity for future application in biotechnology.
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Affiliation(s)
- Yajing Liu
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany; Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Angel Angelov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany; NGS Competence Center Tübingen, Universitätsklinikum Tübingen, Calwerstraße 7, 72076 Tübingen, Germany
| | - Maria Übelacker
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Melanie Baudrexl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Gregor-Mendel-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Broder Rühmann
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany.
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Han R, Baudrexl M, Ludwig C, Berezina OV, Rykov SV, Liebl W. Identification of a novel xanthan-binding module of a multi-modular Cohnella sp. xanthanase. Front Microbiol 2024; 15:1386552. [PMID: 38596379 PMCID: PMC11002231 DOI: 10.3389/fmicb.2024.1386552] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024] Open
Abstract
A new strain of xanthan-degrading bacteria identified as Cohnella sp. has been isolated from a xanthan thickener for food production. The strain was able to utilize xanthan as the only carbon source and to reduce the viscosity of xanthan-containing medium during cultivation. Comparative analysis of the secretomes of Cohnella sp. after growth on different media led to the identification of a xanthanase designated as CspXan9, which was isolated after recombinant production in Escherichia coli. CspXan9 could efficiently degrade the β-1,4-glucan backbone of xanthan after previous removal of pyruvylated mannose residues from the ends of the native xanthan side chains by xanthan lyase treatment (XLT-xanthan). Compared with xanthanase from Paenibacillus nanensis, xanthanase CspXan9 had a different module composition at the N- and C-terminal ends. The main putative oligosaccharides released from XLT-xanthan by CspXan9 cleavage were tetrasaccharides and octasaccharides. To explore the functions of the N- and C-terminal regions of the enzyme, truncated variants lacking some of the non-catalytic modules (CspXan9-C, CspXan9-N, CspXan9-C-N) were produced. Enzyme assays with the purified deletion derivatives, which all contained the catalytic glycoside hydrolase family 9 (GH9) module, demonstrated substantially reduced specific activity on XLT-xanthan of CspXan9-C-N compared with full-length CspXan9. The C-terminal module of CspXan9 was found to represent a novel carbohydrate-binding module of family CBM66 with binding affinity for XLT-xanthan, as was shown by native affinity polyacrylamide gel electrophoresis in the presence of various polysaccharides. The only previously known binding function of a CBM66 member is exo-type binding to the non-reducing fructose ends of the β-fructan polysaccharides inulin and levan.
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Affiliation(s)
- Rui Han
- Chair of Microbiology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Melanie Baudrexl
- Chair of Microbiology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences, Technical University of Munich, Freising, Germany
| | | | - Sergey V. Rykov
- National Research Centre “Kurchatov Institute”, Moscow, Russia
| | - Wolfgang Liebl
- Chair of Microbiology, School of Life Sciences, Technical University of Munich, Freising, Germany
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5
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Yu MSC, Chiang DM, Reithmair M, Meidert A, Brandes F, Schelling G, Ludwig C, Meng C, Kirchner B, Zenner C, Muller L, Pfaffl MW. The proteome of bacterial membrane vesicles in Escherichia coli-a time course comparison study in two different media. Front Microbiol 2024; 15:1361270. [PMID: 38510998 PMCID: PMC10954253 DOI: 10.3389/fmicb.2024.1361270] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/21/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction Bacteria inhabit the in- and outside of the human body, such as skin, gut or the oral cavity where they play an innoxious, beneficial or even pathogenic role. It is well known that bacteria can secrete membrane vesicles (MVs) like eukaryotic cells with extracellular vesicles (EVs). Several studies indicate that bacterial membrane vesicles (bMVs) play a crucial role in microbiome-host interactions. However, the composition of such bMVs and their functionality under different culture conditions are still largely unknown. Methods To gain a better insight into bMVs, we investigated the composition and functionality of E. coli (DSM 105380) bMVs from the culture media Lysogeny broth (LB) and RPMI 1640 throughout the different phases of growth (lag-, log- and stationary-phase). bMVs from three time points (8 h, 54 h, and 168 h) and two media (LB and RPMI 1640) were isolated by ultracentrifugation and analyzed using nanoparticle tracking analysis (NTA), cryogenic electron microscopy (Cryo-EM), conventional transmission electron microscopy (TEM) and mass spectrometry-based proteomics (LC-MS/MS). Furthermore, we examined pro-inflammatory cytokines IL-1β and IL-8 in the human monocyte cell line THP-1 upon bMV treatment. Results Particle numbers increased with inoculation periods. The bMV morphologies in Cryo-EM/TEM were similar at each time point and condition. Using proteomics, we identified 140 proteins, such as the common bMV markers OmpA and GroEL, present in bMVs isolated from both media and at all time points. Additionally, we were able to detect growth-condition-specific proteins. Treatment of THP-1 cells with bMVs of all six groups lead to significantly high IL-1β and IL-8 expressions. Conclusion Our study showed that the choice of medium and the duration of culturing significantly influence both E. coli bMV numbers and protein composition. Our TEM/Cryo-EM results demonstrated the presence of intact E. coli bMVs. Common E. coli proteins, including OmpA, GroEL, and ribosome proteins, can consistently be identified across all six tested growth conditions. Furthermore, our functional assays imply that bMVs isolated from the six groups retain their function and result in comparable cytokine induction.
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Affiliation(s)
- Mia S. C. Yu
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Dapi Menglin Chiang
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
- Institute of Human Genetics, University Hospital, LMU Munich, Munich, Germany
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Marlene Reithmair
- Institute of Human Genetics, University Hospital, LMU Munich, Munich, Germany
| | - Agnes Meidert
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany
| | - Florian Brandes
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany
| | - Gustav Schelling
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Benedikt Kirchner
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
- Institute of Human Genetics, University Hospital, LMU Munich, Munich, Germany
| | - Christian Zenner
- Intestinal Microbiome, ZIEL – Institute for Food & Health, School of Life Sciences, Technical University of Munich (TUM), Freising, Germany
| | - Laurent Muller
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital of Basel, Basel, Switzerland
| | - Michael W. Pfaffl
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
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6
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Hoermann B, Dürr EM, Ludwig C, Ercan M, Köhn M. A strategy to disentangle direct and indirect effects on (de)phosphorylation by chemical modulators of the phosphatase PP1 in complex cellular contexts. Chem Sci 2024; 15:2792-2804. [PMID: 38404380 PMCID: PMC10882499 DOI: 10.1039/d3sc04746f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/12/2024] [Indexed: 02/27/2024] Open
Abstract
Chemical activators and inhibitors are useful probes to identify substrates and downstream effects of enzymes; however, due to the complex signaling environment within cells, it is challenging to distinguish between direct and indirect effects. This is particularly the case for phosphorylation, where a single (de)phosphorylation event can trigger rapid changes in many other phosphorylation sites. An additional complication arises when a single catalytic entity, which acts in the form of many different holoenzymes with different substrates, is activated or inhibited, as it is unclear which holoenzymes are affected, and in turn which of their substrates are (de)phosphorylated. Direct target engaging MS-based technologies to study targets of drugs do not address these challenges. Here, we tackle this by studying the modulation of protein phosphatase-1 (PP1) activity by PP1-disrupting peptides (PDPs), as well as their selectivity toward PP1, by using a combination of mass spectrometry-based experiments. By combining cellular treatment with the PDP with in vitro dephosphorylation by the enzyme, we identify high confidence substrate candidates and begin to separate direct and indirect effects. Together with experiments analyzing which holoenzymes are particularly susceptible to this treatment, we obtain insights into the effect of the modulator on the complex network of protein (de)phosphorylation. This strategy holds promise for enhancing our understanding of PP1 in particular and, due to the broad applicability of the workflow and the MS-based read-out, of chemical modulators with complex mode of action in general.
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Affiliation(s)
- Bernhard Hoermann
- Faculty of Biology, Institute of Biology III, University of Freiburg Freiburg Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg Freiburg Germany
| | - Eva-Maria Dürr
- Faculty of Biology, Institute of Biology III, University of Freiburg Freiburg Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg Freiburg Germany
| | - Christina Ludwig
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM) Freising Germany
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM) Freising Germany
| | - Melda Ercan
- Faculty of Biology, Institute of Biology III, University of Freiburg Freiburg Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg Freiburg Germany
| | - Maja Köhn
- Faculty of Biology, Institute of Biology III, University of Freiburg Freiburg Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg Freiburg Germany
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7
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Voronina L, Fleischmann F, Šimunović J, Ludwig C, Novokmet M, Žigman M. Probing Blood Plasma Protein Glycosylation with Infrared Spectroscopy. Anal Chem 2024. [PMID: 38324652 PMCID: PMC10882574 DOI: 10.1021/acs.analchem.3c03589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The health state of an individual is closely linked to the glycosylation patterns of his or her blood plasma proteins. However, obtaining this information requires cost- and time-efficient analytical methods. We put forward infrared spectroscopy, which allows label-free analysis of protein glycosylation but so far has only been applied to analysis of individual proteins. Although spectral information does not directly provide the molecular structure of the glycans, it is sensitive to changes therein and covers all types of glycosidic linkages. Combining single-step ion exchange chromatography with infrared spectroscopy, we developed a workflow that enables the separation and analysis of major protein classes in blood plasma. Our results demonstrate that infrared spectroscopy can identify different patterns and global levels of glycosylation of intact plasma proteins. To showcase the strengths and limitations of the proposed approach, we compare the glycoforms of human and bovine alpha-1-acid glycoproteins, which exhibit highly variable global levels of glycosylation. To independently evaluate our conclusions, the glycan moieties of human alpha-1-acid glycoprotein were further analyzed using an established glycomics workflow. Importantly, the chromatographic separation of blood plasma improves the detection of aberrant glycoforms of a given protein as compared to infrared spectroscopy of bulk plasma. The presented approach allows a time-efficient comparison of glycosylation patterns of multiple plasma proteins, opening new avenues for biomedical probing.
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Affiliation(s)
- Liudmila Voronina
- Ludwig Maximilian University of Munich, Garching 85748, Germany
- Max Planck Institute of Quantum Optics, Garching 85748, Germany
| | - Frank Fleischmann
- Ludwig Maximilian University of Munich, Garching 85748, Germany
- Max Planck Institute of Quantum Optics, Garching 85748, Germany
| | - Jelena Šimunović
- Glycoscience Research Laboratory, Genos Ltd., Zagreb 10000, Croatia
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising 85354, Germany
| | - Mislav Novokmet
- Glycoscience Research Laboratory, Genos Ltd., Zagreb 10000, Croatia
| | - Mihaela Žigman
- Ludwig Maximilian University of Munich, Garching 85748, Germany
- Max Planck Institute of Quantum Optics, Garching 85748, Germany
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8
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Kardell O, von Toerne C, Merl-Pham J, König AC, Blindert M, Barth TK, Mergner J, Ludwig C, Tüshaus J, Eckert S, Müller SA, Breimann S, Giesbertz P, Bernhardt AM, Schweizer L, Albrecht V, Teupser D, Imhof A, Kuster B, Lichtenthaler SF, Mann M, Cox J, Hauck SM. Multicenter Collaborative Study to Optimize Mass Spectrometry Workflows of Clinical Specimens. J Proteome Res 2024; 23:117-129. [PMID: 38015820 PMCID: PMC10775142 DOI: 10.1021/acs.jproteome.3c00473] [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: 07/31/2023] [Revised: 11/02/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023]
Abstract
The foundation for integrating mass spectrometry (MS)-based proteomics into systems medicine is the development of standardized start-to-finish and fit-for-purpose workflows for clinical specimens. An essential step in this pursuit is to highlight the common ground in a diverse landscape of different sample preparation techniques and liquid chromatography-mass spectrometry (LC-MS) setups. With the aim to benchmark and improve the current best practices among the proteomics MS laboratories of the CLINSPECT-M consortium, we performed two consecutive round-robin studies with full freedom to operate in terms of sample preparation and MS measurements. The six study partners were provided with two clinically relevant sample matrices: plasma and cerebrospinal fluid (CSF). In the first round, each laboratory applied their current best practice protocol for the respective matrix. Based on the achieved results and following a transparent exchange of all lab-specific protocols within the consortium, each laboratory could advance their methods before measuring the same samples in the second acquisition round. Both time points are compared with respect to identifications (IDs), data completeness, and precision, as well as reproducibility. As a result, the individual performances of participating study centers were improved in the second measurement, emphasizing the effect and importance of the expert-driven exchange of best practices for direct practical improvements.
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Affiliation(s)
- Oliver Kardell
- Metabolomics
and Proteomics Core (MPC), Helmholtz Zentrum
München,German Research Center for Environmental Health (GmbH), Munich 80939, Germany
| | - Christine von Toerne
- Metabolomics
and Proteomics Core (MPC), Helmholtz Zentrum
München,German Research Center for Environmental Health (GmbH), Munich 80939, Germany
| | - Juliane Merl-Pham
- Metabolomics
and Proteomics Core (MPC), Helmholtz Zentrum
München,German Research Center for Environmental Health (GmbH), Munich 80939, Germany
| | - Ann-Christine König
- Metabolomics
and Proteomics Core (MPC), Helmholtz Zentrum
München,German Research Center for Environmental Health (GmbH), Munich 80939, Germany
| | - Marcel Blindert
- Metabolomics
and Proteomics Core (MPC), Helmholtz Zentrum
München,German Research Center for Environmental Health (GmbH), Munich 80939, Germany
| | - Teresa K. Barth
- Clinical
Protein Analysis Unit (ClinZfP), Biomedical Center (BMC), Faculty
of Medicine, Ludwig-Maximilians-University
(LMU) Munich, Großhaderner Straße 9, Martinsried 82152, Germany
| | - Julia Mergner
- Bavarian
Center for Biomolecular Mass Spectrometry at Klinikum Rechts der Isar
(BayBioMS@MRI), Technical University of
Munich, Munich 80333, Germany
| | - Christina Ludwig
- Bavarian
Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of
Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Johanna Tüshaus
- Chair
of Proteomics and Bioanalytics, Technical
University of Munich, Freising 85354, Germany
| | - Stephan Eckert
- Chair
of Proteomics and Bioanalytics, Technical
University of Munich, Freising 85354, Germany
| | - Stephan A. Müller
- German
Center
for Neurodegenerative Diseases (DZNE) Munich, DZNE, Munich 81377, Germany
- Neuroproteomics,
School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich 81675, Germany
| | - Stephan Breimann
- German
Center
for Neurodegenerative Diseases (DZNE) Munich, DZNE, Munich 81377, Germany
- Neuroproteomics,
School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich 81675, Germany
| | - Pieter Giesbertz
- German
Center
for Neurodegenerative Diseases (DZNE) Munich, DZNE, Munich 81377, Germany
- Neuroproteomics,
School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich 81675, Germany
| | - Alexander M. Bernhardt
- German
Center
for Neurodegenerative Diseases (DZNE) Munich, DZNE, Munich 81377, Germany
- Department
of Neurology, Ludwig-Maximilians-Universität
München, Munich 80539, Germany
| | - Lisa Schweizer
- Department
of Proteomics and Signal Transduction, Max-Planck
Institute of Biochemistry, Martinsried 82152, Germany
| | - Vincent Albrecht
- Department
of Proteomics and Signal Transduction, Max-Planck
Institute of Biochemistry, Martinsried 82152, Germany
| | - Daniel Teupser
- Institute
of Laboratory Medicine, University Hospital,
LMU Munich, Munich 81377, Germany
| | - Axel Imhof
- Clinical
Protein Analysis Unit (ClinZfP), Biomedical Center (BMC), Faculty
of Medicine, Ludwig-Maximilians-University
(LMU) Munich, Großhaderner Straße 9, Martinsried 82152, Germany
| | - Bernhard Kuster
- Bavarian
Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of
Life Sciences, Technical University of Munich, Freising 85354, Germany
- Chair
of Proteomics and Bioanalytics, Technical
University of Munich, Freising 85354, Germany
| | - Stefan F. Lichtenthaler
- German
Center
for Neurodegenerative Diseases (DZNE) Munich, DZNE, Munich 81377, Germany
- Neuroproteomics,
School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich 81675, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich 81377, Germany
| | - Matthias Mann
- Department
of Proteomics and Signal Transduction, Max-Planck
Institute of Biochemistry, Martinsried 82152, Germany
| | - Jürgen Cox
- Computational Systems
Biochemistry Research Group, Max-Planck
Institute of Biochemistry, Martinsried 82152, Germany
| | - Stefanie M. Hauck
- Metabolomics
and Proteomics Core (MPC), Helmholtz Zentrum
München,German Research Center for Environmental Health (GmbH), Munich 80939, Germany
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9
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Van Bael S, Ludwig C, Baggerman G, Temmerman L. Identification and Targeted Quantification of Endogenous Neuropeptides in the Nematode Caenorhabditis elegans Using Mass Spectrometry. Methods Mol Biol 2024; 2758:341-373. [PMID: 38549024 DOI: 10.1007/978-1-0716-3646-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
The nematode Caenorhabditis elegans lends itself as an excellent model organism for peptidomics studies. Its ease of cultivation and quick generation time make it suitable for high-throughput studies. The nervous system, with its 302 neurons, is probably the best-known and studied endocrine tissue. Moreover, its neuropeptidergic signaling pathways display numerous similarities with those observed in other metazoans. Here, we describe two label-free approaches for neuropeptidomics in C. elegans: one for discovery purposes, and another for targeted quantification and comparisons of neuropeptide levels between different samples. Starting from a detailed peptide extraction procedure, we here outline the liquid chromatography tandem mass spectrometry (LC-MS/MS) setup and describe subsequent data analysis approaches.
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Affiliation(s)
- Sven Van Bael
- Department of Biology, Animal Physiology & Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Geert Baggerman
- Center for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Liesbet Temmerman
- Department of Biology, Animal Physiology & Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium.
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10
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Wiese C, Abele M, Al B, Altmann M, Steiner A, Kalbfuß N, Strohmayr A, Ravikumar R, Park CH, Brunschweiger B, Meng C, Facher E, Ehrhardt DW, Falter-Braun P, Wang ZY, Ludwig C, Assaad FF. Regulation of adaptive growth decisions via phosphorylation of the TRAPPII complex in Arabidopsis. bioRxiv 2023:2023.04.24.537966. [PMID: 37986925 PMCID: PMC10659361 DOI: 10.1101/2023.04.24.537966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Plants often adapt to adverse or stress conditions via differential growth. The trans-Golgi Network (TGN) has been implicated in stress responses, but it is not clear in what capacity it mediates adaptive growth decisions. In this study, we assess the role of the TGN in stress responses by exploring the interactome of the Transport Protein Particle II (TRAPPII) complex, required for TGN structure and function. We identified physical and genetic interactions between TRAPPII and shaggy-like kinases (GSK3/AtSKs). Kinase assays and pharmacological inhibition provided in vitro and in vivo evidence that AtSKs target the TRAPPII-specific subunit AtTRS120/TRAPPC9. GSK3/AtSK phosphorylation sites in AtTRS120/TRAPPC9 were mutated, and the resulting AtTRS120 phosphovariants subjected to a variety of single and multiple stress conditions in planta . The non-phosphorylatable TRS120 mutant exhibited enhanced adaptation to multiple stress conditions and to osmotic stress whereas the phosphomimetic version was less resilient. Higher order inducible trappii atsk mutants had a synthetically enhanced defect in root gravitropism. Our results suggest that the TRAPPII phosphostatus mediates adaptive responses to abiotic cues. AtSKs are multifunctional kinases that integrate a broad range of signals. Similarly, the TRAPPII interactome is vast and considerably enriched in signaling components. An AtSK-TRAPPII interaction would integrate all levels of cellular organization and instruct the TGN, a central and highly discriminate cellular hub, as to how to mobilize and allocate resources to optimize growth and survival under limiting or adverse conditions.
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11
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Noszka M, Strzałka A, Muraszko J, Kolenda R, Meng C, Ludwig C, Stingl K, Zawilak-Pawlik A. Profiling of the Helicobacter pylori redox switch HP1021 regulon using a multi-omics approach. Nat Commun 2023; 14:6715. [PMID: 37872172 PMCID: PMC10593804 DOI: 10.1038/s41467-023-42364-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/09/2023] [Indexed: 10/25/2023] Open
Abstract
The gastric human pathogen Helicobacter pylori has developed mechanisms to combat stress factors, including reactive oxygen species (ROS). Here, we present a comprehensive study on the redox switch protein HP1021 regulon combining transcriptomic, proteomic and DNA-protein interactions analyses. Our results indicate that HP1021 modulates H. pylori's response to oxidative stress. HP1021 controls the transcription of 497 genes, including 407 genes related to response to oxidative stress. 79 proteins are differently expressed in the HP1021 deletion mutant. HP1021 controls typical ROS response pathways (katA, rocF) and less canonical ones, particularly DNA uptake and central carbohydrate metabolism. HP1021 is a molecular regulator of competence in H. pylori, as HP1021-dependent repression of the comB DNA uptake genes is relieved under oxidative conditions, increasing natural competence. Furthermore, HP1021 controls glucose consumption by directly regulating the gluP transporter and has an important impact on maintaining the energetic balance in the cell.
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Affiliation(s)
- Mateusz Noszka
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Agnieszka Strzałka
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Jakub Muraszko
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Rafał Kolenda
- Department of Biochemistry and Molecular Biology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- Quadram Institute Biosciences, Norwich Research Park, Norwich, UK
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Kerstin Stingl
- Department of Biological Safety, National Reference Laboratory for Campylobacter, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Anna Zawilak-Pawlik
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.
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12
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Parmar BS, Kieswetter A, Geens E, Vandewyer E, Ludwig C, Temmerman L. azyx-1 is a new gene that overlaps with zyxin and affects its translation in C. elegans, impacting muscular integrity and locomotion. PLoS Biol 2023; 21:e3002300. [PMID: 37713439 PMCID: PMC10575671 DOI: 10.1371/journal.pbio.3002300] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/13/2023] [Accepted: 08/16/2023] [Indexed: 09/17/2023] Open
Abstract
Overlapping genes are widely prevalent; however, their expression and consequences are poorly understood. Here, we describe and functionally characterize a novel zyx-1 overlapping gene, azyx-1, with distinct regulatory functions in Caenorhabditis elegans. We observed conservation of alternative open reading frames (ORFs) overlapping the 5' region of zyxin family members in several animal species, and find shared sites of azyx-1 and zyxin proteoform expression in C. elegans. In line with a standard ribosome scanning model, our results support cis regulation of zyx-1 long isoform(s) by upstream initiating azyx-1a. Moreover, we report on a rare observation of trans regulation of zyx-1 by azyx-1, with evidence of increased ZYX-1 upon azyx-1 overexpression. Our results suggest a dual role for azyx-1 in influencing zyx-1 proteoform heterogeneity and highlight its impact on C. elegans muscular integrity and locomotion.
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Affiliation(s)
- Bhavesh S. Parmar
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Amanda Kieswetter
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Ellen Geens
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Elke Vandewyer
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technische Universität München, München, Germany
| | - Liesbet Temmerman
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
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13
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Janda M, Rybak K, Krassini L, Meng C, Feitosa-Junior O, Stigliano E, Szulc B, Sklenar J, Menke FL, Malone JG, Brachmann A, Klingl A, Ludwig C, Robatzek S. Biophysical and proteomic analyses of Pseudomonas syringae pv. tomato DC3000 extracellular vesicles suggest adaptive functions during plant infection. mBio 2023; 14:e0358922. [PMID: 37366628 PMCID: PMC10470744 DOI: 10.1128/mbio.03589-22] [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: 01/06/2023] [Accepted: 05/03/2023] [Indexed: 06/28/2023] Open
Abstract
Vesiculation is a process employed by Gram-negative bacteria to release extracellular vesicles (EVs) into the environment. EVs from pathogenic bacteria play functions in host immune modulation, elimination of host defenses, and acquisition of nutrients from the host. Here, we observed EV production of the bacterial speck disease causal agent, Pseudomonas syringae pv. tomato (Pto) DC3000, as outer membrane vesicle release. Mass spectrometry identified 369 proteins enriched in Pto DC3000 EVs. The EV samples contained known immunomodulatory proteins and could induce plant immune responses mediated by bacterial flagellin. Having identified two biomarkers for EV detection, we provide evidence for Pto DC3000 releasing EVs during plant infection. Bioinformatic analysis of the EV-enriched proteins suggests a role for EVs in antibiotic defense and iron acquisition. Thus, our data provide insights into the strategies this pathogen may use to develop in a plant environment. IMPORTANCE The release of extracellular vesicles (EVs) into the environment is ubiquitous among bacteria. Vesiculation has been recognized as an important mechanism of bacterial pathogenesis and human disease but is poorly understood in phytopathogenic bacteria. Our research addresses the role of bacterial EVs in plant infection. In this work, we show that the causal agent of bacterial speck disease, Pseudomonas syringae pv. tomato, produces EVs during plant infection. Our data suggest that EVs may help the bacteria to adapt to environments, e.g., when iron could be limiting such as the plant apoplast, laying the foundation for studying the factors that phytopathogenic bacteria use to thrive in the plant environment.
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Affiliation(s)
- Martin Janda
- LMU Munich Biocenter, Ludwig-Maximilian-University of Munich, Munich, Germany
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czechia
- Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Katarzyna Rybak
- LMU Munich Biocenter, Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Laura Krassini
- LMU Munich Biocenter, Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Gregor-Mendel-Strasse, Freising, United Kingdom
| | | | - Egidio Stigliano
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Beata Szulc
- LMU Munich Biocenter, Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Jan Sklenar
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Frank L.H. Menke
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Jacob G. Malone
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andreas Brachmann
- LMU Munich Biocenter, Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Andreas Klingl
- LMU Munich Biocenter, Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Gregor-Mendel-Strasse, Freising, United Kingdom
| | - Silke Robatzek
- LMU Munich Biocenter, Ludwig-Maximilian-University of Munich, Munich, Germany
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
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14
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Schirmer T, Ludwig C, Scherf KA. Proteomic Characterization of Wheat Protein Fractions Taken at Different Baking Conditions. J Agric Food Chem 2023; 71:12899-12909. [PMID: 37582505 PMCID: PMC10473044 DOI: 10.1021/acs.jafc.3c02100] [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] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/22/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023]
Abstract
Food processing conditions affect the structure, solubility, and therefore accurate detection of gluten proteins. We investigated the influence of dough, bread, and pretzel making on the composition of different wheat protein fractions obtained by Osborne fractionation. The albumin/globulin, gliadin, and glutenin fractions from flour, dough, crispbread, bread, and pretzel were analyzed using RP-HPLC, SDS-PAGE, and untargeted nanoLC-MS/MS. This approach enabled an in-depth profiling of the fractionated proteomes and related compositional changes to processing conditions (mixing, heat, and alkali treatment). Overall, heat treatment demonstrated the most pronounced effect. Label-free quantitation revealed significant changes in the relative abundances of 82 proteins within the fractions of bread crumb and crust in comparison to flour. Certain gluten proteins showed shifts or reductions in particular fractions, indicating their incorporation into the gluten network through SS and non-SS cross-links. Other gluten proteins were enriched, suggesting their limited involvement in the gluten network formation.
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Affiliation(s)
- Tanja
Miriam Schirmer
- Leibniz-Institute
for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany
| | - Christina Ludwig
- Bavarian
Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Gregor-Mendel-Straße 4, 85354 Freising, Germany
| | - Katharina Anne Scherf
- Leibniz-Institute
for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany
- Department
of Bioactive and Functional Food Chemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Adenauerring 20 a, 76131 Karlsruhe, Germany
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15
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Mondino A, Ludwig C, Menchaca C, Russell K, Simon KE, Griffith E, Kis A, Lascelles BDX, Gruen ME, Olby NJ. Development and validation of a sleep questionnaire, SNoRE 3.0, to evaluate sleep in companion dogs. Sci Rep 2023; 13:13340. [PMID: 37587172 PMCID: PMC10432410 DOI: 10.1038/s41598-023-40048-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/03/2023] [Indexed: 08/18/2023] Open
Abstract
Disturbances in the sleep-wake cycle are a debilitating, yet rather common condition not only in humans, but also in family dogs. While there is an emerging need for easy-to-use tools to document sleep alterations (in order to ultimately treat and/or prevent them), the veterinary tools which yield objective data (e.g. polysomnography, activity monitors) are both labor intensive and expensive. In this study, we developed a modified version of a previously used sleep questionnaire (SNoRE) and determined criterion validity in companion dogs against polysomnography and physical activity monitors (PAMs). Since a negative correlation between sleep time and cognitive performance in senior dogs has been demonstrated, we evaluated the correlation between the SNoRE scores and the Canine Dementia Scale (CADES, which includes a factor concerning sleep). There was a significant correlation between SNoRE 3.0 questionnaire scores and polysomnography data (latency to NREM sleep, ρ = 0.507, p < 0.001) as well as PAMs' data (activity between 1:00 and 3:00 AM, p < 0.05). There was a moderate positive correlation between the SNoRE 3.0 scores and the CADES scores (ρ = 0.625, p < 0.001). Additionally, the questionnaire structure was validated by a confirmatory factor analysis, and it also showed an adequate test-retest reliability. In conclusion the present paper describes a valid and reliable questionnaire tool, that can be used as a cost-effective way to monitor dog sleep in clinical settings.
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Affiliation(s)
- A Mondino
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA
| | - C Ludwig
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA
| | - C Menchaca
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA
| | - K Russell
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA
| | - K E Simon
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA
| | - E Griffith
- Department of Statistics, North Carolina State University, Raleigh, NC, 27606, USA
| | - A Kis
- Institute of Cognitive Neuroscience and Psychology, Research Centre for Natural Sciences, Budapest, Hungary
| | - B D X Lascelles
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA
- Translational Research in Pain, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA
| | - M E Gruen
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA
| | - N J Olby
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA.
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16
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Abele M, Doll E, Bayer FP, Meng C, Lomp N, Neuhaus K, Scherer S, Kuster B, Ludwig C. Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes. Mol Cell Proteomics 2023; 22:100612. [PMID: 37391045 PMCID: PMC10407251 DOI: 10.1016/j.mcpro.2023.100612] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/18/2023] [Accepted: 06/26/2023] [Indexed: 07/02/2023] Open
Abstract
Bacteria are the most abundant and diverse organisms among the kingdoms of life. Due to this excessive variance, finding a unified, comprehensive, and safe workflow for quantitative bacterial proteomics is challenging. In this study, we have systematically evaluated and optimized sample preparation, mass spectrometric data acquisition, and data analysis strategies in bacterial proteomics. We investigated workflow performances on six representative species with highly different physiologic properties to mimic bacterial diversity. The best sample preparation strategy was a cell lysis protocol in 100% trifluoroacetic acid followed by an in-solution digest. Peptides were separated on a 30-min linear microflow liquid chromatography gradient and analyzed in data-independent acquisition mode. Data analysis was performed with DIA-NN using a predicted spectral library. Performance was evaluated according to the number of identified proteins, quantitative precision, throughput, costs, and biological safety. With this rapid workflow, over 40% of all encoded genes were detected per bacterial species. We demonstrated the general applicability of our workflow on a set of 23 taxonomically and physiologically diverse bacterial species. We could confidently identify over 45,000 proteins in the combined dataset, of which 30,000 have not been experimentally validated before. Our work thereby provides a valuable resource for the microbial scientific community. Finally, we grew Escherichia coli and Bacillus cereus in replicates under 12 different cultivation conditions to demonstrate the high-throughput suitability of the workflow. The proteomic workflow we present in this manuscript does not require any specialized equipment or commercial software and can be easily applied by other laboratories to support and accelerate the proteomic exploration of the bacterial kingdom.
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Affiliation(s)
- Miriam Abele
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany; Division of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Etienne Doll
- Division of Microbial Ecology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Florian P Bayer
- Division of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Nina Lomp
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Klaus Neuhaus
- Division of Microbial Ecology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; Core Facility Microbiome, ZIEL - Institute for Food & Health, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Siegfried Scherer
- Division of Microbial Ecology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany; Division of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
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17
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Yang Y, Steidele CE, Rössner C, Löffelhardt B, Kolb D, Leisen T, Zhang W, Ludwig C, Felix G, Seidl MF, Becker A, Nürnberger T, Hahn M, Gust B, Gross H, Hückelhoven R, Gust AA. Convergent evolution of plant pattern recognition receptors sensing cysteine-rich patterns from three microbial kingdoms. Nat Commun 2023; 14:3621. [PMID: 37336953 DOI: 10.1038/s41467-023-39208-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 06/03/2023] [Indexed: 06/21/2023] Open
Abstract
The Arabidopsis thaliana Receptor-Like Protein RLP30 contributes to immunity against the fungal pathogen Sclerotinia sclerotiorum. Here we identify the RLP30-ligand as a small cysteine-rich protein (SCP) that occurs in many fungi and oomycetes and is also recognized by the Nicotiana benthamiana RLP RE02. However, RLP30 and RE02 share little sequence similarity and respond to different parts of the native/folded protein. Moreover, some Brassicaceae other than Arabidopsis also respond to a linear SCP peptide instead of the folded protein, suggesting that SCP is an eminent immune target that led to the convergent evolution of distinct immune receptors in plants. Surprisingly, RLP30 shows a second ligand specificity for a SCP-nonhomologous protein secreted by bacterial Pseudomonads. RLP30 expression in N. tabacum results in quantitatively lower susceptibility to bacterial, fungal and oomycete pathogens, thus demonstrating that detection of immunogenic patterns by Arabidopsis RLP30 is involved in defense against pathogens from three microbial kingdoms.
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Affiliation(s)
- Yuankun Yang
- Department of Plant Biochemistry, Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University of Tübingen, Tübingen, Germany.
| | - Christina E Steidele
- Department of Plant Biochemistry, Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University of Tübingen, Tübingen, Germany
- Chair of Phytopathology, TUM School of Life Sciences, Technische Universität München, Freising-Weihenstephan, Germany
| | - Clemens Rössner
- Institute of Botany, Developmental Biology of Plants, Justus-Liebig-University Gießen, Gießen, Germany
| | - Birgit Löffelhardt
- Department of Plant Biochemistry, Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University of Tübingen, Tübingen, Germany
| | - Dagmar Kolb
- Department of Plant Biochemistry, Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University of Tübingen, Tübingen, Germany
| | - Thomas Leisen
- Department of Biology, Phytopathology group, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Weiguo Zhang
- Department of Plant Biochemistry, Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University of Tübingen, Tübingen, Germany
- Faculty of Life Science, Northwest University, Xi'an, China
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technische Universität München, Freising-Weihenstephan, Germany
| | - Georg Felix
- Department of Plant Biochemistry, Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University of Tübingen, Tübingen, Germany
| | - Michael F Seidl
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
| | - Annette Becker
- Institute of Botany, Developmental Biology of Plants, Justus-Liebig-University Gießen, Gießen, Germany
| | - Thorsten Nürnberger
- Department of Plant Biochemistry, Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University of Tübingen, Tübingen, Germany
| | - Matthias Hahn
- Department of Biology, Phytopathology group, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Bertolt Gust
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard-Karls-University of Tübingen, Tübingen, Germany
| | - Harald Gross
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard-Karls-University of Tübingen, Tübingen, Germany
| | - Ralph Hückelhoven
- Chair of Phytopathology, TUM School of Life Sciences, Technische Universität München, Freising-Weihenstephan, Germany
| | - Andrea A Gust
- Department of Plant Biochemistry, Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University of Tübingen, Tübingen, Germany.
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Sun G, Liao J, Kurze E, Hoffmann TD, Steinchen W, McGraphery K, Habegger R, Marek L, Catici DAM, Ludwig C, Jing T, Hoffmann T, Song C, Schwab W. Apocarotenoids are allosteric effectors of a dimeric plant glycosyltransferase involved in defense and lignin formation. New Phytol 2023; 238:2080-2098. [PMID: 36908092 DOI: 10.1111/nph.18875] [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] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 03/02/2023] [Indexed: 05/04/2023]
Abstract
Glycosyltransferases are nature's versatile tools to tailor the functionalities of proteins, carbohydrates, lipids, and small molecules by transferring sugars. Prominent substrates are hydroxycoumarins such as scopoletin, which serve as natural plant protection agents. Similarly, C13-apocarotenoids, which are oxidative degradation products of carotenoids/xanthophylls, protect plants by repelling pests and attracting pest predators. We show that C13-apocarotenoids interact with the plant glycosyltransferase NbUGT72AY1 and induce conformational changes in the enzyme catalytic center ultimately reducing its inherent UDP-α-d-glucose glucohydrolase activity and increasing its catalytic activity for productive hydroxycoumarin substrates. By contrast, C13-apocarotenoids show no effect on the catalytic activity toward monolignol lignin precursors, which are competitive substrates. In vivo studies in tobacco plants (Nicotiana benthamiana) confirmed increased glycosylation activity upon apocarotenoid supplementation. Thus, hydroxycoumarins and apocarotenoids represent specialized damage-associated molecular patterns, as they each provide precise information about the plant compartments damaged by pathogen attack. The molecular basis for the C13-apocarotenoid-mediated interplay of two plant protective mechanisms and their function as allosteric enhancers opens up potential applications of the natural products in agriculture and pharmaceutical industry.
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Affiliation(s)
- Guangxin Sun
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Jieren Liao
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Elisabeth Kurze
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Timothy D Hoffmann
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Karl-von-Frisch-Straße 14, 35043, Marburg, Germany
| | - Kate McGraphery
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Ruth Habegger
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Ludwig Marek
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Dragana A M Catici
- Center for Protein Assemblies (CPA), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences Weihenstephan, Technische Universität München, Gregor-Mendel-Str. 4, 85354, Freising, Germany
| | - Tingting Jing
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, 230036, Hefei, Anhui, China
| | - Thomas Hoffmann
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Chuankui Song
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, 230036, Hefei, Anhui, China
| | - Wilfried Schwab
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
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Bimmer M, Reimer M, Klingl A, Ludwig C, Zollfrank C, Liebl W, Ehrenreich A. Analysis of cellulose synthesis in a high-producing acetic acid bacterium Komagataeibacter hansenii. Appl Microbiol Biotechnol 2023; 107:2947-2967. [PMID: 36930278 PMCID: PMC10106347 DOI: 10.1007/s00253-023-12461-z] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023]
Abstract
Bacterial cellulose (BC) represents a renewable biomaterial with unique properties promising for biotechnology and biomedicine. Komagataeibacter hansenii ATCC 53,582 is a well-characterized high-yield producer of BC used in the industry. Its genome encodes three distinct cellulose synthases (CS), bcsAB1, bcsAB2, and bcsAB3, which together with genes for accessory proteins are organized in operons of different complexity. The genetic foundation of its high cellulose-producing phenotype was investigated by constructing chromosomal in-frame deletions of the CSs and of two predicted regulatory diguanylate cyclases (DGC), dgcA and dgcB. Proteomic characterization suggested that BcsAB1 was the decisive CS because of its high expression and its exclusive contribution to the formation of microcrystalline cellulose. BcsAB2 showed a lower expression level but contributes significantly to the tensile strength of BC and alters fiber diameter significantly as judged by scanning electron microscopy. Nevertheless, no distinct extracellular polymeric substance (EPS) from this operon was identified after static cultivation. Although transcription of bcsAB3 was observed, expression of the protein was below the detection limit of proteome analysis. Alike BcsAB2, deletion of BcsAB3 resulted in a visible reduction of the cellulose fiber diameter. The high abundance of BcsD and the accessory proteins CmcAx, CcpAx, and BglxA emphasizes their importance for the proper formation of the cellulosic network. Characterization of deletion mutants lacking the DGC genes dgcA and dgcB suggests a new regulatory mechanism of cellulose synthesis and cell motility in K. hansenii ATCC 53,582. Our findings form the basis for rational tailoring of the characteristics of BC. KEY POINTS: • BcsAB1 induces formation of microcrystalline cellulose fibers. • Modifications by BcsAB2 and BcsAB3 alter diameter of cellulose fibers. • Complex regulatory network of DGCs on cellulose pellicle formation and motility.
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Affiliation(s)
- Martin Bimmer
- School of Life Sciences, Technical University of Munich, Emil-Ramann-Straße 4, 85354, Freising, Germany
| | - Martin Reimer
- Technical University of Munich, Campus Straubing, Schulgasse 16, 94315, Straubing, Germany
| | - Andreas Klingl
- Plant Development, Ludwig-Maximilans-Universität München, Großhaderner Str.2, 82152, BiozentrumPlanegg-Martinsried, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences, Technical University of Munich, Gregor-Mendel-Straße 4, 85354, Freising, Germany
| | - Cordt Zollfrank
- Technical University of Munich, Campus Straubing, Schulgasse 16, 94315, Straubing, Germany
| | - Wolfgang Liebl
- School of Life Sciences, Technical University of Munich, Emil-Ramann-Straße 4, 85354, Freising, Germany
| | - Armin Ehrenreich
- School of Life Sciences, Technical University of Munich, Emil-Ramann-Straße 4, 85354, Freising, Germany.
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Berry BJ, Vodičková A, Müller-Eigner A, Meng C, Ludwig C, Kaeberlein M, Peleg S, Wojtovich AP. Optogenetic rejuvenation of mitochondrial membrane potential extends C. elegans lifespan. Nat Aging 2023; 3:157-161. [PMID: 36873708 PMCID: PMC9980297 DOI: 10.1038/s43587-022-00340-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mitochondrial dysfunction plays a central role in aging but the exact biological causes are still being determined. Here, we show that optogenetically increasing mitochondrial membrane potential during adulthood using a light-activated proton pump improves age-associated phenotypes and extends lifespan in C. elegans. Our findings provide direct causal evidence that rescuing the age-related decline in mitochondrial membrane potential is sufficient to slow the rate of aging and extend healthspan and lifespan.
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Affiliation(s)
- Brandon J Berry
- University of Washington, Department of Laboratory Medicine & Pathology, Seattle WA, 98195, United States of America
| | - Anežka Vodičková
- University of Rochester Medical Center, Department of Anesthesiology and Perioperative Medicine, 575 Elmwood Ave., Rochester NY, 14642 Box 711/604. United States of America
| | - Annika Müller-Eigner
- Research Group Epigenetics, Metabolism and Longevity, Research Institute for Farm Animal Biology (FBN), Dummerstorf, 18147, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, 85354, Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, 85354, Freising, Germany
| | - Matt Kaeberlein
- University of Washington, Department of Laboratory Medicine & Pathology, Seattle WA, 98195, United States of America
| | - Shahaf Peleg
- Research Group Epigenetics, Metabolism and Longevity, Research Institute for Farm Animal Biology (FBN), Dummerstorf, 18147, Germany
| | - Andrew P Wojtovich
- University of Rochester Medical Center, Department of Anesthesiology and Perioperative Medicine, 575 Elmwood Ave., Rochester NY, 14642 Box 711/604. United States of America
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Wu C, Mori M, Abele M, Banaei-Esfahani A, Zhang Z, Okano H, Aebersold R, Ludwig C, Hwa T. Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves. Nat Microbiol 2023; 8:347-359. [PMID: 36737588 PMCID: PMC9994330 DOI: 10.1038/s41564-022-01310-w] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/15/2022] [Indexed: 02/05/2023]
Abstract
Bacterial fitness depends on adaptability to changing environments. In rich growth medium, which is replete with amino acids, Escherichia coli primarily expresses protein synthesis machineries, which comprise ~40% of cellular proteins and are required for rapid growth. Upon transition to minimal medium, which lacks amino acids, biosynthetic enzymes are synthesized, eventually reaching ~15% of cellular proteins when growth fully resumes. We applied quantitative proteomics to analyse the timing of enzyme expression during such transitions, and established a simple positive relation between the onset time of enzyme synthesis and the fractional enzyme 'reserve' maintained by E. coli while growing in rich media. We devised and validated a coarse-grained kinetic model that quantitatively captures the enzyme recovery kinetics in different pathways, solely on the basis of proteomes immediately preceding the transition and well after its completion. Our model enables us to infer regulatory strategies underlying the 'as-needed' gene expression programme adopted by E. coli.
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Affiliation(s)
- Chenhao Wu
- Department of Physics, U.C. San Diego, La Jolla, CA, USA.
| | - Matteo Mori
- Department of Physics, U.C. San Diego, La Jolla, CA, USA
| | - Miriam Abele
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Freising, Germany
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Amir Banaei-Esfahani
- Department of Biology, Institute of Molecular Systems Biology, ETH, Zurich, Switzerland
| | - Zhongge Zhang
- Division of Biological Sciences, U.C. San Diego, La Jolla, CA, USA
| | - Hiroyuki Okano
- Department of Physics, U.C. San Diego, La Jolla, CA, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Freising, Germany.
| | - Terence Hwa
- Department of Physics, U.C. San Diego, La Jolla, CA, USA.
- Division of Biological Sciences, U.C. San Diego, La Jolla, CA, USA.
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22
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Cockx B, Van Bael S, Boelen R, Vandewyer E, Yang H, Le TA, Dalzell JJ, Beets I, Ludwig C, Lee J, Temmerman L. Mass Spectrometry-Driven Discovery of Neuropeptides Mediating Nictation Behavior of Nematodes. Mol Cell Proteomics 2023; 22:100479. [PMID: 36481452 PMCID: PMC9881375 DOI: 10.1016/j.mcpro.2022.100479] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/27/2022] [Accepted: 11/20/2022] [Indexed: 12/12/2022] Open
Abstract
Neuropeptides regulate animal physiology and behavior, making them widely studied targets of functional genetics research. While the field often relies on differential -omics approaches to build hypotheses, no such method exists for neuropeptidomics. It would nonetheless be valuable for studying behaviors suspected to be regulated by neuropeptides, especially when little information is otherwise available. This includes nictation, a phoretic strategy of Caenorhabditis elegans dauers that parallels host-finding strategies of infective juveniles of many pathogenic nematodes. We here developed a targeted peptidomics method for the model organism C. elegans and show that 161 quantified neuropeptides are more abundant in its dauer stage compared with L3 juveniles. Many of these have orthologs in the commercially relevant pathogenic nematode Steinernema carpocapsae, in whose infective juveniles, we identified 126 neuropeptides in total. Through further behavioral genetics experiments, we identify flp-7 and flp-11 as novel regulators of nictation. Our work advances knowledge on the genetics of nictation behavior and adds comparative neuropeptidomics as a tool to functional genetics workflows.
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Affiliation(s)
- Bram Cockx
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Sven Van Bael
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Rose Boelen
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Elke Vandewyer
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Heeseung Yang
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Tuan Anh Le
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Johnathan J Dalzell
- School of Biological Sciences, Queen's University Belfast, Northern Ireland, United Kingdom
| | - Isabel Beets
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Liesbet Temmerman
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium.
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Balakrishnan R, Mori M, Segota I, Zhang Z, Aebersold R, Ludwig C, Hwa T. Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria. Science 2022; 378:eabk2066. [PMID: 36480614 PMCID: PMC9804519 DOI: 10.1126/science.abk2066] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein concentrations are set by a complex interplay between gene-specific regulatory processes and systemic factors, including cell volume and shared gene expression machineries. Elucidating this interplay is crucial for discerning and designing gene regulatory systems. We quantitatively characterized gene-specific and systemic factors that affect transcription and translation genome-wide for Escherichia coli across many conditions. The results revealed two design principles that make regulation of gene expression insulated from concentrations of shared machineries: RNA polymerase activity is fine-tuned to match translational output, and translational characteristics are similar across most messenger RNAs (mRNAs). Consequently, in bacteria, protein concentration is set primarily at the promoter level. A simple mathematical formula relates promoter activities and protein concentrations across growth conditions, enabling quantitative inference of gene regulation from omics data.
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Affiliation(s)
- Rohan Balakrishnan
- Department of Physics, University of California at San Diego, La Jolla, California 92093-0374
| | - Matteo Mori
- Department of Physics, University of California at San Diego, La Jolla, California 92093-0374
| | - Igor Segota
- Departments of Medicine and Pharmacology, University of California at San Diego, La Jolla, California 92093
| | - Zhongge Zhang
- Section of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093
| | - Ruedi Aebersold
- Faculty of Science, University of Zurich, Zurich, Switzerland.,Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Terence Hwa
- Department of Physics, University of California at San Diego, La Jolla, California 92093-0374.,Section of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093.,CORRESPONDING AUTHOR: Terence Hwa ()
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Chebib S, Meng C, Ludwig C, Bergmann KC, Becker S, Dierend W, Schwab W. Identification of allergenomic signatures in allergic and well-tolerated apple genotypes using LC-MS/MS. Food Chem (Oxf) 2022; 4:100111. [PMID: 35592704 PMCID: PMC9110896 DOI: 10.1016/j.fochms.2022.100111] [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] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 04/12/2022] [Accepted: 05/02/2022] [Indexed: 04/12/2023]
Abstract
The apple fruit (Malus domestica L. Borkh) is one of the most popular fruits worldwide. Beyond their beneficial properties, apples contain proteins that trigger allergic reactions in susceptible consumers. Mal d1 to d4 are allergens present in a variety of different isoforms in apples. In this study, we used proteomics to quantify all four Mal d proteins in 52 apple genotypes with varying allergenic potentials. A total of 195, 17, 14, and 18 peptides were found to be related to Mal d1, d2, d3, and d4 proteins, respectively of which 25 different Mal d proteins could be unambiguously identified. The allergenic potential of the Mal d isoforms was characterized by comparing the isoform abundance with the allergenic score of genotypes from oral challenge tests. The detected Mal d peptides presumably have different IgE binding properties and could be used as potential molecular markers to discriminate between hypoallergenic and hyperallergenic cultivars.
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Affiliation(s)
- Soraya Chebib
- Biotechnology of Natural Products, Technical University Munich, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University Munich, Gregor-Mendel-Straße 4, 85354 Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University Munich, Gregor-Mendel-Straße 4, 85354 Freising, Germany
| | - Karl-Christian Bergmann
- Allergy-Centre-Charité, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany
| | - Sylvia Becker
- European Centre Allergy Research Foundation, Robert-Koch-Platz 7, 10115 Berlin, Germany
| | - Werner Dierend
- Faculty of Agricultural Science and Landscape Architecture, Fruit Science, University of Applied Sciences Osnabrück, Oldenburger Landstr. 24, 49090 Osnabrück, Germany
| | - Wilfried Schwab
- Biotechnology of Natural Products, Technical University Munich, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
- Corresponding author.
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Fuertes-Perez S, Abele M, Ludwig C, Vogel RF, Hilgarth M. Impact of Modified Atmospheres on Growth and Metabolism of Meat-Spoilage Relevant Photobacterium spp. as Predicted by Comparative Proteomics. Front Microbiol 2022; 13:866629. [PMID: 35722325 PMCID: PMC9201721 DOI: 10.3389/fmicb.2022.866629] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/12/2022] [Indexed: 11/25/2022] Open
Abstract
Modified atmosphere packaging (MAP) is a common strategy to selectively prevent the growth of certain species of meat spoiling bacteria. This study aimed to determine the impact of high oxygen MAP (70% O2, 30% CO2, red and white meats) and oxygen-free MAP (70% N2, 30% CO2, also white meat and seafood) on preventing the growth of spoiling photobacteria on meat. Growth of Photobacterium carnosum and P. phosphoreum was monitored in a meat simulation media under different gas mixtures of nitrogen, oxygen, and carbon dioxide, and samples were taken during exponential growth for a comparative proteomic analysis. Growth under air atmosphere appears optimal, particularly for P. carnosum. Enhanced protein accumulation affected energy metabolism, respiration, oxygen consuming reactions, and lipid usage. However, all the other atmospheres show some degree of growth reduction. An increase in oxygen concentration leads to an increase in enzymes counteracting oxidative stress for both species and enhancement of heme utilization and iron-sulfur cluster assembly proteins for P. phosphoreum. Absence of oxygen appears to switch the metabolism toward fermentative pathways where either ribose (P. phosphoreum) or glycogen (P. carnosum) appear to be the preferred substrates. Additionally, it promotes the use of alternative electron donors/acceptors, mainly formate and nitrate/nitrite. Stress response is manifested as an enhanced accumulation of enzymes that is able to produce ammonia (e.g., carbonic anhydrase, hydroxylamine reductase) and regulate osmotic stress. Our results suggest that photobacteria do not sense the environmental levels of carbon dioxide, but rather adapt to their own anaerobic metabolism. The regulation in presence of carbon dioxide is limited and strain-specific under anaerobic conditions. However, when oxygen at air-like concentration (21%) is present together with carbon dioxide (30%), the oxidative stress appears enhanced compared to air conditions (very low carbon dioxide), as explained if both gases have a synergistic effect. This is further supported by the increase in oxygen concentration in the presence of carbon dioxide. The atmosphere is able to fully inhibit P. carnosum, heavily reduce P. phosphoreum growth in vitro, and trigger diversification of energy production with higher energetic cost, highlighting the importance of concomitant bacteria for their growth on raw meat under said atmosphere.
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Affiliation(s)
- Sandra Fuertes-Perez
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Munich, Germany
| | - Miriam Abele
- Bayerisches Zentrum für Biomolekulare Massenspektrometrie (BayBioMS), Technische Universität München, Munich, Germany
| | - Christina Ludwig
- Bayerisches Zentrum für Biomolekulare Massenspektrometrie (BayBioMS), Technische Universität München, Munich, Germany
| | - Rudi F Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Munich, Germany
| | - Maik Hilgarth
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Munich, Germany
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Stefanski AL, Rincon-Arevalo H, Schrezenmeier E, Karberg K, Szelinski F, Ritter J, Jahresdoerfer B, Schrezenmeier H, Ludwig C, Chen Y, Claußnitzer A, Lino A, Dörner T. POS0050 B CELL CHARACTERISTICS AT BASELINE PREDICT HUMORAL RESPONSE UPON SARS-CoV-2 VACCINATION AMONG PATIENTS TREATED WITH RITUXIMAB. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BackgroundVaccination is considered efficient in controlling infections incl. SARS-CoV-2. Prior studies showed that patients receiving rituximab (RTX) with low B cell counts are at increased infectious risk (1) and risk of inadequate vaccination responses (2, 3). Thus, the ability to further define and predict vaccination responses in these patients may guide their optimal protection.ObjectivesTo assess predictive biomarkers of vaccination responses upon SARS-CoV-2 vaccination in RTX treated patients.MethodsB cell characteristics before vaccination were evaluated to predict responses in 15 patients with autoimmune inflammatory rheumatic diseases receiving RTX. 11 patients with rheumatoid arthritis on other therapies (RA), 11 kidney transplant recipients (KTR) and 15 healthy volunteers (HC) served as controls. A multidimensional analysis of B cell subsets and a correlation matrix were performed to identify predictive biomarkers.ResultsSignificant differences regarding absolute B cell counts and specific subset distribution pattern between the groups were validated at baseline. Here, the majority of B cells from vaccination responders of the RTX group (RTX IgG+) comprised naïve and transitional B cells, whereas vaccination non-responders (RTX IgG-) carried preferentially plasmablasts and double negative (CD27-IgD-) B cells (Figure 1). Moreover, there was a positive correlation between neutralizing antibodies and absolute B cell numbers with B cells expressing HLA-DR and CXCR5 (involved in antigen presentation and germinal center formation) as well as an inverse correlation with CD95 expression and CD21low expression (marker for activation and exhaustion) on B cells.ConclusionSubstantial repopulation of naïve B cells upon RTX therapy appears to be essential for an adequate vaccination response requiring germinal center formation. In contrast, expression of exhaustion markers (CD21low, CXCR5-, CD95+) indicate negative predictors of vaccination responses. These results may guide optimized vaccination strategies in RTX treated patients clearly requiring antigen-inexperienced B cells for appropriate protection.References[1]Sparks JA, Wallace ZS, Seet AM, Gianfrancesco MA, Izadi Z, Hyrich KL, et al. Associations of baseline use of biologic or targeted synthetic DMARDs with COVID-19 severity in rheumatoid arthritis: Results from the COVID-19 Global Rheumatology Alliance physician registry. Annals of the Rheumatic Diseases. 2021;80(9):1137-46.[2]Stefanski AL, Rincon-Arevalo H, Schrezenmeier E, Karberg K, Szelinski F, Ritter J, et al. B cell numbers predict humoral and cellular response upon SARS-CoV-2 vaccination among patients treated with rituximab. Arthritis & Rheumatology. Accepted Author Manuscript.[3]Mrak D, Tobudic S, Koblischke M, Graninger M, Radner H, Sieghart D, et al. SARS-CoV-2 vaccination in rituximab-treated patients: B cells promote humoral immune responses in the presence of T-cell-mediated immunity. Annals of the rheumatic diseases. 2021;80(10):1345-50.Disclosure of InterestsNone declared
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Stegmann M, Zecua-Ramirez P, Ludwig C, Lee HS, Peterson B, Nimchuk ZL, Belkhadir Y, Hückelhoven R. RGI-GOLVEN signaling promotes cell surface immune receptor abundance to regulate plant immunity. EMBO Rep 2022; 23:e53281. [PMID: 35229426 PMCID: PMC9066070 DOI: 10.15252/embr.202153281] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 05/17/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 11/26/2022] Open
Abstract
Plant immune responses must be tightly controlled for proper allocation of resources for growth and development. In plants, endogenous signaling peptides regulate developmental and growth‐related processes. Recent research indicates that some of these peptides also have regulatory functions in the control of plant immune responses. This classifies these peptides as phytocytokines as they show analogies with metazoan cytokines. However, the mechanistic basis for phytocytokine‐mediated regulation of plant immunity remains largely elusive. Here, we identify GOLVEN2 (GLV2) peptides as phytocytokines in Arabidopsis thaliana. GLV2 signaling enhances sensitivity of plants to elicitation with immunogenic bacterial elicitors and contributes to resistance against virulent bacterial pathogens. GLV2 is perceived by ROOT MERISTEM GROWTH FACTOR 1 INSENSITIVE (RGI) receptors. RGI mutants show reduced elicitor sensitivity and enhanced susceptibility to bacterial infection. RGI3 forms ligand‐induced complexes with the pattern recognition receptor (PRR) FLAGELLIN SENSITIVE 2 (FLS2), suggesting that RGIs are part of PRR signaling platforms. GLV2‐RGI signaling promotes PRR abundance independent of transcriptional regulation and controls plant immunity via a previously undescribed mechanism of phytocytokine activity.
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Affiliation(s)
- Martin Stegmann
- Phytopathology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Patricia Zecua-Ramirez
- Phytopathology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Ho-Seok Lee
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Brenda Peterson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Youssef Belkhadir
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Ralph Hückelhoven
- Phytopathology, School of Life Sciences, Technical University of Munich, Freising, Germany
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28
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Stegmann M, Zecua-Ramirez P, Ludwig C, Lee HS, Peterson B, Nimchuk ZL, Belkhadir Y, Hückelhoven R. RGI-GOLVEN signaling promotes cell surface immune receptor abundance to regulate plant immunity. EMBO Rep 2022; 23:e53281. [PMID: 35229426 DOI: 10.1101/2021.01.29.428839] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 05/23/2023] Open
Abstract
Plant immune responses must be tightly controlled for proper allocation of resources for growth and development. In plants, endogenous signaling peptides regulate developmental and growth-related processes. Recent research indicates that some of these peptides also have regulatory functions in the control of plant immune responses. This classifies these peptides as phytocytokines as they show analogies with metazoan cytokines. However, the mechanistic basis for phytocytokine-mediated regulation of plant immunity remains largely elusive. Here, we identify GOLVEN2 (GLV2) peptides as phytocytokines in Arabidopsis thaliana. GLV2 signaling enhances sensitivity of plants to elicitation with immunogenic bacterial elicitors and contributes to resistance against virulent bacterial pathogens. GLV2 is perceived by ROOT MERISTEM GROWTH FACTOR 1 INSENSITIVE (RGI) receptors. RGI mutants show reduced elicitor sensitivity and enhanced susceptibility to bacterial infection. RGI3 forms ligand-induced complexes with the pattern recognition receptor (PRR) FLAGELLIN SENSITIVE 2 (FLS2), suggesting that RGIs are part of PRR signaling platforms. GLV2-RGI signaling promotes PRR abundance independent of transcriptional regulation and controls plant immunity via a previously undescribed mechanism of phytocytokine activity.
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Affiliation(s)
- Martin Stegmann
- Phytopathology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Patricia Zecua-Ramirez
- Phytopathology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Ho-Seok Lee
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Brenda Peterson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Youssef Belkhadir
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Ralph Hückelhoven
- Phytopathology, School of Life Sciences, Technical University of Munich, Freising, Germany
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29
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Müller-Eigner A, Sanz-Moreno A, de-Diego I, Venkatasubramani AV, Langhammer M, Gerlini R, Rathkolb B, Aguilar-Pimentel A, Klein-Rodewald T, Calzada-Wack J, Becker L, Palma-Vera S, Gille B, Forne I, Imhof A, Meng C, Ludwig C, Koch F, Heiker JT, Kuhla A, Caton V, Brenmoehl J, Reyer H, Schoen J, Fuchs H, Gailus-Durner V, Hoeflich A, de Angelis MH, Peleg S. Dietary intervention improves health metrics and life expectancy of the genetically obese Titan mouse. Commun Biol 2022; 5:408. [PMID: 35505192 PMCID: PMC9065075 DOI: 10.1038/s42003-022-03339-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 04/04/2022] [Indexed: 01/02/2023] Open
Abstract
Suitable animal models are essential for translational research, especially in the case of complex, multifactorial conditions, such as obesity. The non-inbred mouse (Mus musculus) line Titan, also known as DU6, is one of the world’s longest selection experiments for high body mass and was previously described as a model for metabolic healthy (benign) obesity. The present study further characterizes the geno- and phenotypes of this non-inbred mouse line and tests its suitability as an interventional obesity model. In contrast to previous findings, our data suggest that Titan mice are metabolically unhealthy obese and short-lived. Line-specific patterns of genetic invariability are in accordance with observed phenotypic traits. Titan mice also show modifications in the liver transcriptome, proteome, and epigenome linked to metabolic (dys)regulations. Importantly, dietary intervention partially reversed the metabolic phenotype in Titan mice and significantly extended their life expectancy. Therefore, the Titan mouse line is a valuable resource for translational and interventional obesity research. This study further characterizes the non-inbred Titan (also known as DU6) mouse line, which could be a useful model for obesity research.
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Affiliation(s)
- Annika Müller-Eigner
- Research Group Epigenetics, Metabolism and Longevity, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Adrián Sanz-Moreno
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environment and Health (GmbH), 85764, Neuherberg, Germany
| | - Irene de-Diego
- Research Group Epigenetics, Metabolism and Longevity, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | | | - Martina Langhammer
- Institute Genetics and Biometry, Lab Animal Facility, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Raffaele Gerlini
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environment and Health (GmbH), 85764, Neuherberg, Germany.,German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Birgit Rathkolb
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environment and Health (GmbH), 85764, Neuherberg, Germany.,German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany.,Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-University Munich, 81377, Munich, Germany
| | - Antonio Aguilar-Pimentel
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environment and Health (GmbH), 85764, Neuherberg, Germany
| | - Tanja Klein-Rodewald
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environment and Health (GmbH), 85764, Neuherberg, Germany
| | - Julia Calzada-Wack
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environment and Health (GmbH), 85764, Neuherberg, Germany
| | - Lore Becker
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environment and Health (GmbH), 85764, Neuherberg, Germany
| | - Sergio Palma-Vera
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Benedikt Gille
- Research Group Epigenetics, Metabolism and Longevity, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Ignasi Forne
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians University, 82152, Planegg-Martinsried, Germany
| | - Axel Imhof
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians University, 82152, Planegg-Martinsried, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, 85354, Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, 85354, Freising, Germany
| | - Franziska Koch
- Institute of Nutritional Physiology, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - John T Heiker
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Angela Kuhla
- Institute for Experimental Surgery, Rostock University Medical Center, Rostock, Germany
| | - Vanessa Caton
- Institute for Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Julia Brenmoehl
- Institute for Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Henry Reyer
- Institute for Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Jennifer Schoen
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany.,Department of Reproduction Biology, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environment and Health (GmbH), 85764, Neuherberg, Germany
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environment and Health (GmbH), 85764, Neuherberg, Germany
| | - Andreas Hoeflich
- Institute for Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environment and Health (GmbH), 85764, Neuherberg, Germany.,German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany.,Chair of Experimental Genetics, TUM School of Life Sciences (SoLS), Technische Universität München, 85354, Freising, Germany
| | - Shahaf Peleg
- Research Group Epigenetics, Metabolism and Longevity, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany. .,Institute of Neuroregeneration and Neurorehabilitation of Qingdao University, Qingdao, China.
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Bockwoldt JA, Meng C, Ludwig C, Kupetz M, Ehrmann MA. Proteomic Analysis Reveals Enzymes for β-D-Glucan Formation and Degradation in Levilactobacillus brevis TMW 1.2112. Int J Mol Sci 2022; 23:ijms23063393. [PMID: 35328813 PMCID: PMC8951740 DOI: 10.3390/ijms23063393] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 02/01/2023] Open
Abstract
Bacterial exopolysaccharide (EPS) formation is crucial for biofilm formation, for protection against environmental factors, or as storage compounds. EPSs produced by lactic acid bacteria (LAB) are appropriate for applications in food fermentation or the pharmaceutical industry, yet the dynamics of formation and degradation thereof are poorly described. This study focuses on carbohydrate active enzymes, including glycosyl transferases (GT) and glycoside hydrolases (GH), and their roles in the formation and potential degradation of O2-substituted (1,3)-β-D-glucan of Levilactobacillus (L.) brevis TMW 1.2112. The fermentation broth of L. brevis TMW 1.2112 was analyzed for changes in viscosity, β-glucan, and D-glucose concentrations during the exponential, stationary, and early death phases. While the viscosity reached its maximum during the stationary phase and subsequently decreased, the β-glucan concentration only increased to a plateau. Results were correlated with secretome and proteome data to identify involved enzymes and pathways. The suggested pathway for β-glucan biosynthesis involved a β-1,3 glucan synthase (GT2) and enzymes from maltose phosphorylase (MP) operons. The decreased viscosity appeared to be associated with cell lysis as the β-glucan concentration did not decrease, most likely due to missing extracellular carbohydrate active enzymes. In addition, an operon was discovered containing known moonlighting genes, all of which were detected in both proteome and secretome samples.
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Affiliation(s)
- Julia A. Bockwoldt
- Lehrstuhl für Mikrobiologie, Technische Universität München, 85354 Freising, Germany;
| | - Chen Meng
- Bayerisches Zentrum für Biomolekulare Massenspektrometrie (BayBioMS), Technische Universität München, 85354 Freising, Germany; (C.M.); (C.L.)
| | - Christina Ludwig
- Bayerisches Zentrum für Biomolekulare Massenspektrometrie (BayBioMS), Technische Universität München, 85354 Freising, Germany; (C.M.); (C.L.)
| | - Michael Kupetz
- Lehrstuhl für Brau- und Getränketechnologie, Technische Universität München, 85354 Freising, Germany;
| | - Matthias A. Ehrmann
- Lehrstuhl für Mikrobiologie, Technische Universität München, 85354 Freising, Germany;
- Correspondence:
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31
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Kreitmeier M, Ardern Z, Abele M, Ludwig C, Scherer S, Neuhaus K. Spotlight on alternative frame coding: Two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection. iScience 2022; 25:103844. [PMID: 35198897 PMCID: PMC8850804 DOI: 10.1016/j.isci.2022.103844] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/14/2021] [Accepted: 01/27/2022] [Indexed: 12/13/2022] Open
Abstract
The existence of overlapping genes (OLGs) with significant coding overlaps revolutionizes our understanding of genomic complexity. We report two exceptionally long (957 nt and 1536 nt), evolutionarily novel, translated antisense open reading frames (ORFs) embedded within annotated genes in the pathogenic Gram-negative bacterium Pseudomonas aeruginosa. Both OLG pairs show sequence features consistent with being genes and transcriptional signals in RNA sequencing. Translation of both OLGs was confirmed by ribosome profiling and mass spectrometry. Quantitative proteomics of samples taken during different phases of growth revealed regulation of protein abundances, implying biological functionality. Both OLGs are taxonomically restricted, and likely arose by overprinting within the genus. Evidence for purifying selection further supports functionality. The OLGs reported here, designated olg1 and olg2, are the longest yet proposed in prokaryotes and are among the best attested in terms of translation and evolutionary constraint. These results highlight a potentially large unexplored dimension of prokaryotic genomes. Two novel, very long, overlapping genes were found in Pseudomonas aeruginosa Both overlapping genes, olg1 and olg2, are transcribed, translated, and regulated Mass spectrometry verifies translation of the overlapping and their mother genes Both overlapping genes are taxonomically restricted, but under purifying selection
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Affiliation(s)
- Michaela Kreitmeier
- Chair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Zachary Ardern
- Chair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany.,Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Miriam Abele
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technische Universität München, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technische Universität München, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Siegfried Scherer
- Chair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Klaus Neuhaus
- Core Facility Microbiome, ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
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32
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Phan T, Maity P, Ludwig C, Streit L, Michaelis J, Tsesmelis M, Scharffetter-Kochanek K, Iben S. Nucleolar TFIIE plays a role in ribosomal biogenesis and performance. Nucleic Acids Res 2021; 49:11197-11210. [PMID: 34581812 PMCID: PMC8565312 DOI: 10.1093/nar/gkab866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 09/09/2021] [Accepted: 09/16/2021] [Indexed: 11/29/2022] Open
Abstract
Ribosome biogenesis is a highly energy-demanding process in eukaryotes which requires the concerted action of all three RNA polymerases. In RNA polymerase II transcription, the general transcription factor TFIIH is recruited by TFIIE to the initiation site of protein-coding genes. Distinct mutations in TFIIH and TFIIE give rise to the degenerative disorder trichothiodystrophy (TTD). Here, we uncovered an unexpected role of TFIIE in ribosomal RNA synthesis by RNA polymerase I. With high resolution microscopy we detected TFIIE in the nucleolus where TFIIE binds to actively transcribed rDNA. Mutations in TFIIE affects gene-occupancy of RNA polymerase I, rRNA maturation, ribosomal assembly and performance. In consequence, the elevated translational error rate with imbalanced protein synthesis and turnover results in an increase in heat-sensitive proteins. Collectively, mutations in TFIIE—due to impaired ribosomal biogenesis and translational accuracy—lead to a loss of protein homeostasis (proteostasis) which can partly explain the clinical phenotype in TTD.
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Affiliation(s)
- Tamara Phan
- Department of Dermatology and Allergic Diseases, Ulm University, Ulm, Baden-Württemberg, 89081 Germany
| | - Pallab Maity
- Department of Dermatology and Allergic Diseases, Ulm University, Ulm, Baden-Württemberg, 89081 Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University Munich, Freising, Bavaria 85354, Germany
| | - Lisa Streit
- Institute of Biophysics, Ulm University, Ulm, Baden-Württemberg 89081, Germany
| | - Jens Michaelis
- Institute of Biophysics, Ulm University, Ulm, Baden-Württemberg 89081, Germany
| | - Miltiadis Tsesmelis
- Institute of Physiological Chemistry, Ulm University, Ulm, Baden-Württemberg 89081, Germany
| | | | - Sebastian Iben
- Department of Dermatology and Allergic Diseases, Ulm University, Ulm, Baden-Württemberg, 89081 Germany
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Giannaki M, Ludwig C, Heermann S, Roussa E. Regulation of electrogenic Na + /HCO 3 - cotransporter 1 (NBCe1) function and its dependence on m-TOR mediated phosphorylation of Ser 245. J Cell Physiol 2021; 237:1372-1388. [PMID: 34642952 DOI: 10.1002/jcp.30601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/09/2021] [Accepted: 10/01/2021] [Indexed: 11/09/2022]
Abstract
Astrocytes are pivotal responders to alterations of extracellular pH, primarily by regulation of their principal acid-base transporter, the membrane-bound electrogenic Na+ /bicarbonate cotransporter 1 (NBCe1). Here, we describe amammalian target of rapamycin (mTOR)-dependent and NBCe1-mediated astroglial response to extracellular acidosis. Using primary mouse cortical astrocytes, we investigated the effect of long-term extracellular metabolic acidosis on regulation of NBCe1 and elucidated the underlying molecular mechanisms by immunoblotting, biotinylation of surface proteins, intracellular H+ recording using the H+ -sensitive dye 2',7'-bis-(carboxyethyl)-5-(and-6)-carboxyfluorescein, and phosphoproteomic analysis. The results showed significant increase of NBCe1-mediated recovery of intracellular pH from acidification in WT astrocytes, but not in cortical astrocytes from NBCe1-deficient mice. Acidosis-induced upregulation of NBCe1 activity was prevented following inhibition of mTOR signaling by rapamycin. Yet, during acidosis or following exposure of astrocytes to rapamycin, surface protein abundance of NBCe1 remained -unchanged. Mutational analysis in HeLa cells suggested that NBCe1 activity was dependent on phosphorylation state of Ser245 , a residue conserved in all NBCe1 variants. Moreover, phosphorylation state of Ser245 is regulated by mTOR and is inversely correlated with NBCe1 transport activity. Our results identify pSer245 as a novel regulator of NBCe1 functional expression. We propose that context-dependent and mTOR-mediated multisite phosphorylation of serine residues of NBCe1 is likely to be a potent mechanism contributing to the response of astrocytes to acid/base challenges during pathophysiological conditions.
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Affiliation(s)
- Marina Giannaki
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Medical Faculty, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Stephan Heermann
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Medical Faculty, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Eleni Roussa
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Medical Faculty, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
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Phan T, Maity P, Ludwig C, Streit L, Michaelis J, Scharffetter-Kochanek K, Iben S. 161 Nucleolar TFIIE plays a role in ribosomal biogenesis and performance. J Invest Dermatol 2021. [DOI: 10.1016/j.jid.2021.08.165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Falgenhauer E, von Schönberg S, Meng C, Mückl A, Vogele K, Emslander Q, Ludwig C, Simmel FC. Evaluation of an E. coli Cell Extract Prepared by Lysozyme-Assisted Sonication via Gene Expression, Phage Assembly and Proteomics. Chembiochem 2021; 22:2805-2813. [PMID: 34240805 PMCID: PMC8518995 DOI: 10.1002/cbic.202100257] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/08/2021] [Indexed: 11/08/2022]
Abstract
Over the past decades, starting from crude cell extracts, a variety of successful preparation protocols and optimized reaction conditions have been established for the production of cell-free gene expression systems. One of the crucial steps during the preparation of cell extract-based expression systems is the cell lysis procedure itself, which largely determines the quality of the active components of the extract. Here we evaluate the utility of an E. coli cell extract, which was prepared using a combination of lysozyme incubation and a gentle sonication step. As quality measure, we demonstrate the cell-free expression of YFP at concentrations up to 0.6 mg/mL. In addition, we produced and assembled T7 bacteriophages up to a titer of 108 PFU/mL. State-of-the-art quantitative proteomics was used to compare the produced extracts with each other and with a commercial extract. The differences in protein composition were surprisingly small between lysozyme-assisted sonication (LAS) extracts, but we observed an increase in the release of DNA-binding proteins for increasing numbers of sonication cycles. Proteins taking part in carbohydrate metabolism, glycolysis, amino acid and nucleotide related pathways were found to be more abundant in the LAS extract, while proteins related to RNA modification and processing, DNA modification and replication, transcription regulation, initiation, termination and the TCA cycle were found enriched in the commercial extract.
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Affiliation(s)
- Elisabeth Falgenhauer
- Physics of Synthetic Biological Systems, Physics Department E14Technical University of MunichAm Coulombwall 4a85748GarchingGermany
| | - Sophie von Schönberg
- Physics of Synthetic Biological Systems, Physics Department E14Technical University of MunichAm Coulombwall 4a85748GarchingGermany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS)Technical University of MunichGregor-Mendel-Strasse 485354FreisingGermany
| | - Andrea Mückl
- Physics of Synthetic Biological Systems, Physics Department E14Technical University of MunichAm Coulombwall 4a85748GarchingGermany
| | - Kilian Vogele
- Physics of Synthetic Biological Systems, Physics Department E14Technical University of MunichAm Coulombwall 4a85748GarchingGermany
| | - Quirin Emslander
- Physics of Synthetic Biological Systems, Physics Department E14Technical University of MunichAm Coulombwall 4a85748GarchingGermany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS)Technical University of MunichGregor-Mendel-Strasse 485354FreisingGermany
| | - Friedrich C. Simmel
- Physics of Synthetic Biological Systems, Physics Department E14Technical University of MunichAm Coulombwall 4a85748GarchingGermany
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36
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Keilhoff G, Ludwig C, Pinkernelle J, Lucas B. Effects of Gynostemma pentaphyllum on spinal cord motor neurons and microglial cells in vitro. Acta Histochem 2021; 123:151759. [PMID: 34425524 DOI: 10.1016/j.acthis.2021.151759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/25/2021] [Accepted: 07/11/2021] [Indexed: 11/18/2022]
Abstract
The regenerative capability of spinal cord neurons is limited to impossible. Thus, experimental approaches supporting reconstruction/regeneration are in process. This study focused on the evaluation of the protective potency of an extract from Gynostemma pentaphyllum (GP), a plant used in traditional medicine with anti-oxidative and neuroprotective activities, in vitro on organotypic spinal cord cultures, the motor-neuron-like NSC-34 cell line and the microglial cell line BV-2. Organotypic cultures were mechanically stressed by the slicing procedure and the effect of GP on motor neuron survival and neurite sprouting was tested by immunohistochemistry. NSC-34 cells were neuronal differentiated by using special medium. Afterwards, cell survival (propidium iodide/fluorescein diacetate labeling), proliferation (BrdU-incorporation), and neurite sprouting were evaluated. BV-2 cells were stimulated with LPS/interferon γ and subjected to migration assay and nanoparticle uptake. Cell survival, proliferation and the expression pattern of different microglial activation markers (cFOS, iNOS) as well as transcription factors (PPARγ, YB1) were analyzed. In organotypic cultures, high-dose GP supported survival of motor neurons and especially of the neuronal fiber network. Despite reduced neurodegeneration, however, there was a GP-mediated activation of astro- and microglia. In NSC-34 cells, high-dosed GP had degenerative and anti-proliferative effects, but only in normal medium. Moreover, GP supported the neuro-differentiation ability. In BV-2 cells, high-dosed GP was toxic. In lower dosages, GP affected cell survival and proliferation when combined with LPS/interferon γ. Nanoparticle uptake, migration ability, and the transcription factor PPARγ, however, GP affected directly. The data suggest positive effects of GP on injured spinal motor neurons. Moreover, GP activated microglial cells. The dual role of microglia (protective/detrimental) in neurodegenerative processes required further experiments to enhance the knowledge about GP effects. Therefore, a possible clinical use of GP in spinal cord injuries is still a long way off.
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Affiliation(s)
- Gerburg Keilhoff
- Institute of Biochemistry and Cell Biology, Medical Faculty, Otto-von-Guericke University Magdeburg, Germany.
| | - Christina Ludwig
- Institute of Biochemistry and Cell Biology, Medical Faculty, Otto-von-Guericke University Magdeburg, Germany
| | - Josephine Pinkernelle
- Institute of Biochemistry and Cell Biology, Medical Faculty, Otto-von-Guericke University Magdeburg, Germany
| | - Benjamin Lucas
- Dept. of Trauma Surgery, Medical Faculty, Otto-von-Guericke University Magdeburg, Germany
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Qiang M, Khalid F, Phan T, Ludwig C, Scharffetter-Kochanek K, Iben S. Cockayne Syndrome-Associated CSA and CSB Mutations Impair Ribosome Biogenesis, Ribosomal Protein Stability, and Global Protein Folding. Cells 2021; 10:cells10071616. [PMID: 34203326 PMCID: PMC8306422 DOI: 10.3390/cells10071616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 12/18/2022] Open
Abstract
Cockayne syndrome (CS) is a developmental disorder with symptoms that are typical for the aging body, including subcutaneous fat loss, alopecia, and cataracts. Here, we show that in the cells of CS patients, RNA polymerase I transcription and the processing of the pre-rRNA are disturbed, leading to an accumulation of the 18S-E intermediate. The mature 18S rRNA level is reduced, and isolated ribosomes lack specific ribosomal proteins of the small 40S subunit. Ribosomal proteins are susceptible to unfolding and the CS cell proteome is heat-sensitive, indicating misfolded proteins and an error-prone translation process in CS cells. Pharmaceutical chaperones restored impaired cellular proliferation. Therefore, we provide evidence for severe protein synthesis malfunction, which together with a loss of proteostasis constitutes the underlying pathophysiology in CS.
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Affiliation(s)
- Mingyue Qiang
- Department of Dermatology and Allergic Diseases, Ulm University, Albert-Einstein Allee 23, 89081 Ulm, Germany; (M.Q.); (F.K.); (T.P.); (K.S.-K.)
| | - Fatima Khalid
- Department of Dermatology and Allergic Diseases, Ulm University, Albert-Einstein Allee 23, 89081 Ulm, Germany; (M.Q.); (F.K.); (T.P.); (K.S.-K.)
| | - Tamara Phan
- Department of Dermatology and Allergic Diseases, Ulm University, Albert-Einstein Allee 23, 89081 Ulm, Germany; (M.Q.); (F.K.); (T.P.); (K.S.-K.)
| | - Christina Ludwig
- Bavarian Center for Biomedical Mass Spectrometry, TUM, University of Munich, 85354 Freising, Germany;
| | - Karin Scharffetter-Kochanek
- Department of Dermatology and Allergic Diseases, Ulm University, Albert-Einstein Allee 23, 89081 Ulm, Germany; (M.Q.); (F.K.); (T.P.); (K.S.-K.)
| | - Sebastian Iben
- Department of Dermatology and Allergic Diseases, Ulm University, Albert-Einstein Allee 23, 89081 Ulm, Germany; (M.Q.); (F.K.); (T.P.); (K.S.-K.)
- Correspondence:
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Pal J, Becker AC, Dhamija S, Seiler J, Abdelkarim M, Sharma Y, Behr J, Meng C, Ludwig C, Kuster B, Diederichs S. Systematic analysis of migration factors by MigExpress identifies essential cell migration control genes in non-small cell lung cancer. Mol Oncol 2021; 15:1797-1817. [PMID: 33934493 PMCID: PMC8253088 DOI: 10.1002/1878-0261.12973] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 11/07/2022] Open
Abstract
Cell migration is an essential process in health and in disease, including cancer metastasis. A comprehensive inventory of migration factors is nonetheless lacking-in part due to the difficulty in assessing migration using high-throughput technologies. Hence, there are currently very few screens that systematically reveal factors controlling cell migration. Here, we introduce MigExpress as a platform for the 'identification of Migration control genes by differential Expression'. MigExpress exploits the combination of in-depth molecular profiling and the robust quantitative analysis of migration capacity in a broad panel of samples and identifies migration-associated genes by their differential expression in slow- versus fast-migrating cells. We applied MigExpress to investigate non-small cell lung cancer (NSCLC), which is the most frequent cause of cancer mortality mainly due to metastasis. In 54 NSCLC cell lines, we comprehensively determined mRNA and protein expression. Correlating the transcriptome and proteome profiles with the quantified migration properties led to the discovery and validation of FLNC, DSE, CPA4, TUBB6, and BICC1 as migration control factors in NSCLC cells, which were also negatively correlated with patient survival. Notably, FLNC was the least expressed filamin in NSCLC, but the only one controlling cell migration and correlating with patient survival and metastatic disease stage. In our study, we present MigExpress as a new method for the systematic analysis of migration factors and provide a comprehensive resource of transcriptomic and proteomic data of NSCLC cell lines related to cell migration.
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Affiliation(s)
- Jagriti Pal
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Germany
| | - Andrea C Becker
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Germany
| | - Sonam Dhamija
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Germany.,Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Jeanette Seiler
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mahmoud Abdelkarim
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Germany
| | - Yogita Sharma
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Germany
| | - Jürgen Behr
- Leibniz Institute for Food Systems, Technical University of Munich, Freising, Germany.,Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany.,Chair of Proteomics and Bioanalytics, DKTK Partner Site Munich, Freising, Germany
| | - Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Germany.,Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Mori M, Zhang Z, Banaei‐Esfahani A, Lalanne J, Okano H, Collins BC, Schmidt A, Schubert OT, Lee D, Li G, Aebersold R, Hwa T, Ludwig C. From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions. Mol Syst Biol 2021; 17:e9536. [PMID: 34032011 PMCID: PMC8144880 DOI: 10.15252/msb.20209536] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022] Open
Abstract
Accurate measurements of cellular protein concentrations are invaluable to quantitative studies of gene expression and physiology in living cells. Here, we developed a versatile mass spectrometric workflow based on data-independent acquisition proteomics (DIA/SWATH) together with a novel protein inference algorithm (xTop). We used this workflow to accurately quantify absolute protein abundances in Escherichia coli for > 2,000 proteins over > 60 growth conditions, including nutrient limitations, non-metabolic stresses, and non-planktonic states. The resulting high-quality dataset of protein mass fractions allowed us to characterize proteome responses from a coarse (groups of related proteins) to a fine (individual) protein level. Hereby, a plethora of novel biological findings could be elucidated, including the generic upregulation of low-abundant proteins under various metabolic limitations, the non-specificity of catabolic enzymes upregulated under carbon limitation, the lack of large-scale proteome reallocation under stress compared to nutrient limitations, as well as surprising strain-dependent effects important for biofilm formation. These results present valuable resources for the systems biology community and can be used for future multi-omics studies of gene regulation and metabolic control in E. coli.
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Affiliation(s)
- Matteo Mori
- Department of PhysicsUniversity of California at San DiegoLa JollaCAUSA
| | - Zhongge Zhang
- Section of Molecular BiologyDivision of Biological SciencesUniversity of California at San DiegoLa JollaCAUSA
| | - Amir Banaei‐Esfahani
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Jean‐Benoît Lalanne
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of PhysicsMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Hiroyuki Okano
- Department of PhysicsUniversity of California at San DiegoLa JollaCAUSA
| | - Ben C Collins
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
- School of Biological SciencesQueen's University of BelfastBelfastUK
| | | | - Olga T Schubert
- Department of Human GeneticsUniversity of California, Los AngelesLos AngelesCAUSA
| | - Deok‐Sun Lee
- School of Computational SciencesKorea Institute for Advanced StudySeoulKorea
| | - Gene‐Wei Li
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Ruedi Aebersold
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
- Faculty of ScienceUniversity of ZurichZurichSwitzerland
| | - Terence Hwa
- Department of PhysicsUniversity of California at San DiegoLa JollaCAUSA
- Section of Molecular BiologyDivision of Biological SciencesUniversity of California at San DiegoLa JollaCAUSA
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS)Technical University of Munich (TUM)FreisingGermany
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García MV, García LL, Fescina RC, González AV, Ludwig C, Suarez AG, Fernández JL, Lora CH, León SO, Martino RA. Relationship between suicide attempts of repetition and dependence to the cocaine: Report of clinical case. Eur Psychiatry 2021. [PMCID: PMC9480320 DOI: 10.1192/j.eurpsy.2021.1715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Introduction People with borderline personality disorder are at higher risk of repeating suicidal behavior. At the same time, numerous publications have demonstrated the relationship between cocaine dependence and suicide attempts of repetition. Objectives Review the relationship between cocaine addiction, borderline personality disorder and repeated suicide attempts. Present through a clinical case the effectiveness of a comprehensive and multidisciplinary therapeutic plan with different mental health devices. Methods To review the psychopathological evolution of a patient with a diagnosis of borderline personality disorder; dependence to the cocaine; Harmful alcohol consumption and suicidal behavior from the beginning of follow-up in mental health services to the present. Review the existing scientific evidence on the relationship between cocaine addiction and repeated suicide attempts. Analyze the eficacy of the different treatments available. Results This is a longitudinal and retrospective study of the psychiatric history and evolution of a clinical case since the implementation of an individualized therapeutic program and the favorable results obtained. Intensive outpatient follow-up was carried out for high suicide risk and hospitalization in a psychiatric hospitalization unit, day care centre and therapeutic community. Conclusions At present, the patient remains in abstinence with remission of suicidal ideation. The literature has shown the usefulness of intensive mental health follow-up programs to achieve remission of suicidal ideation and maintain abstinence from illegal substances. Disclosure No significant relationships.
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García MV, Fescina RC, González AV, Ludwig C, Suarez AG, Fernández JL, Lora CH, León SO, García LL. Schizoaffective disorder: Nosological controversies and absence of specific treatment guidelines. Eur Psychiatry 2021. [PMCID: PMC9476068 DOI: 10.1192/j.eurpsy.2021.1441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Introduction Schizoaffective disorder is a psychotic disorder of controversial nosological entity. Affective symptomatology and psychotic features of varying intensity coexist simultaneously in him throughout evolution. The lack of consensus on the existence of this entity determines its diagnostic delay and the absence of specific treatment guidelines. Objectives To review the diagnostic criteria for schizoaffective disorder and the published scientific evidence on the efficacy and safety of the different therapeutic options available. To analyze the efficacy of a multidisciplinary treatment plan implemented in an intensive follow-up program, presenting the evolution of a clinical case. Methods To review the psychiatric history and psychopathological evolution of a patient diagnosed with schizoaffective disorder from the beginning of an intensive follow-up program in a day center to the present. Review the existing scientific evidence on the usefulness of the treatments used in this nosological entity. Results This is a longitudinal and retrospective study of a clinical case in which the areas for improvement are analyzed before implementing a multidisciplinary therapeutic program and the favorable results obtained today. Currently, the patient is euthymic and attenuated and chronic positive and negative symptoms persist that do not interfere with his functionality. Conclusions From the implementation of an individualized, personalized and multidisciplinary maintenance treatment plan, an overall improvement in psychopathological stability and functional recovery is observed. Among the psychopharmacological options in this patient, Paliperidone Long Acting Injection (PLAI) stands out for its long-term efficacy and safety.
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42
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Zhao Y, Schoeps B, Yao D, Zhang Z, Schuck K, Tissen V, Jäger C, Schlitter AM, van der Kammen R, Ludwig C, D'Haese JG, Raulefs S, Maeritz N, Shen S, Zou X, Krüger A, Kleeff J, Michalski CW, Friess H, Innocenti M, Kong B. mTORC1 and mTORC2 Converge on the Arp2/3 Complex to Promote Kras G12D-Induced Acinar-to-Ductal Metaplasia and Early Pancreatic Carcinogenesis. Gastroenterology 2021; 160:1755-1770.e17. [PMID: 33388318 DOI: 10.1053/j.gastro.2020.12.061] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 04/22/2020] [Revised: 12/04/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Oncogenic KrasG12D induces neoplastic transformation of pancreatic acinar cells through acinar-to-ductal metaplasia (ADM), an actin-based morphogenetic process, and drives pancreatic ductal adenocarcinoma (PDAC). mTOR (mechanistic target of rapamycin kinase) complex 1 (mTORC1) and 2 (mTORC2) contain Rptor and Rictor, respectively, and are activated downstream of KrasG12D, thereby contributing to PDAC. Yet, whether and how mTORC1 and mTORC2 impact on ADM and the identity of the actin nucleator(s) mediating such actin rearrangements remain unknown. METHODS A mouse model of inflammation-accelerated KrasG12D-driven early pancreatic carcinogenesis was used. Rptor, Rictor, and Arpc4 (actin-related protein 2/3 complex subunit 4) were conditionally ablated in acinar cells to deactivate the function of mTORC1, mTORC2 and the actin-related protein (Arp) 2/3 complex, respectively. RESULTS We found that mTORC1 and mTORC2 are markedly activated in human and mouse ADM lesions, and cooperate to promote KrasG12D-driven ADM in mice and in vitro. They use the Arp2/3 complex as a common downstream effector to induce the remodeling the actin cytoskeleton leading to ADM. In particular, mTORC1 regulates the translation of Rac1 (Rac family small GTPase 1) and the Arp2/3-complex subunit Arp3, whereas mTORC2 activates the Arp2/3 complex by promoting Akt/Rac1 signaling. Consistently, genetic ablation of the Arp2/3 complex prevents KrasG12D-driven ADM in vivo. In acinar cells, the Arp2/3 complex and its actin-nucleation activity mediated the formation of a basolateral actin cortex, which is indispensable for ADM and pre-neoplastic transformation. CONCLUSIONS Here, we show that mTORC1 and mTORC2 attain a dual, yet nonredundant regulatory role in ADM and early pancreatic carcinogenesis by promoting Arp2/3 complex function. The role of Arp2/3 complex as a common effector of mTORC1 and mTORC2 fills the gap between oncogenic signals and actin dynamics underlying PDAC initiation.
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MESH Headings
- Acinar Cells/enzymology
- Acinar Cells/pathology
- Actin-Related Protein 2-3 Complex/genetics
- Actin-Related Protein 2-3 Complex/metabolism
- Animals
- Carcinoma, Pancreatic Ductal/enzymology
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/pathology
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Disease Models, Animal
- Gene Expression Regulation, Neoplastic
- Humans
- Mechanistic Target of Rapamycin Complex 1/genetics
- Mechanistic Target of Rapamycin Complex 1/metabolism
- Mechanistic Target of Rapamycin Complex 2/genetics
- Mechanistic Target of Rapamycin Complex 2/metabolism
- Metaplasia
- Mice, Inbred C57BL
- Mice, Knockout
- Mutation
- Pancreatic Ducts/enzymology
- Pancreatic Ducts/pathology
- Pancreatic Neoplasms/enzymology
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/pathology
- Proto-Oncogene Proteins p21(ras)/genetics
- Rapamycin-Insensitive Companion of mTOR Protein/genetics
- Rapamycin-Insensitive Companion of mTOR Protein/metabolism
- Regulatory-Associated Protein of mTOR/genetics
- Regulatory-Associated Protein of mTOR/metabolism
- Signal Transduction
- Mice
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Affiliation(s)
- Yamin Zhao
- Department of Surgery, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Benjamin Schoeps
- Institute of Molecular Immunology and Experimental Oncology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Dianbo Yao
- Department of Surgery, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Zhiheng Zhang
- Department of Surgery, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Kathleen Schuck
- Department of Surgery, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Vivien Tissen
- Department of Surgery, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Carsten Jäger
- Department of Surgery, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | | | - Rob van der Kammen
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Jan G D'Haese
- Department of General, Visceral, and Transplantation, Ludwig Maximilians University, Munich, Germany
| | - Susanne Raulefs
- Department of Surgery, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Nadja Maeritz
- Department of Surgery, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Shanshan Shen
- Department of Gastroenterology, the Affiliated Drum Tower Hospital of Nanjing University, Medical School, Nanjing, China
| | - Xiaoping Zou
- Department of Gastroenterology, the Affiliated Drum Tower Hospital of Nanjing University, Medical School, Nanjing, China
| | - Achim Krüger
- Institute of Molecular Immunology and Experimental Oncology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Jörg Kleeff
- Department of Visceral, Vascular and Endocrine Surgery, Martin Luther University Halle-Wittenberg, Germany
| | | | - Helmut Friess
- Department of Surgery, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Metello Innocenti
- Heidelberg University Biochemistry Center, Heidelberg University, Heidelberg, Germany
| | - Bo Kong
- Department of Surgery, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany; Department of Gastroenterology, the Affiliated Drum Tower Hospital of Nanjing University, Medical School, Nanjing, China; German Cancer Consortium at the partner site Munich, Munich, Germany.
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Stenton SL, Sheremet NL, Catarino CB, Andreeva NA, Assouline Z, Barboni P, Barel O, Berutti R, Bychkov I, Caporali L, Capristo M, Carbonelli M, Cascavilla ML, Charbel Issa P, Freisinger P, Gerber S, Ghezzi D, Graf E, Heidler J, Hempel M, Heon E, Itkis YS, Javasky E, Kaplan J, Kopajtich R, Kornblum C, Kovacs-Nagy R, Krylova TD, Kunz WS, La Morgia C, Lamperti C, Ludwig C, Malacarne PF, Maresca A, Mayr JA, Meisterknecht J, Nevinitsyna TA, Palombo F, Pode-Shakked B, Shmelkova MS, Strom TM, Tagliavini F, Tzadok M, van der Ven AT, Vignal-Clermont C, Wagner M, Zakharova EY, Zhorzholadze NV, Rozet JM, Carelli V, Tsygankova PG, Klopstock T, Wittig I, Prokisch H. Impaired complex I repair causes recessive Leber's hereditary optic neuropathy. J Clin Invest 2021; 131:138267. [PMID: 33465056 PMCID: PMC7954600 DOI: 10.1172/jci138267] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [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: 03/19/2020] [Accepted: 01/14/2021] [Indexed: 12/12/2022] Open
Abstract
Leber’s hereditary optic neuropathy (LHON) is the most frequent mitochondrial disease and was the first to be genetically defined by a point mutation in mitochondrial DNA (mtDNA). A molecular diagnosis is achieved in up to 95% of cases, the vast majority of which are accounted for by 3 mutations within mitochondrial complex I subunit–encoding genes in the mtDNA (mtLHON). Here, we resolve the enigma of LHON in the absence of pathogenic mtDNA mutations. We describe biallelic mutations in a nuclear encoded gene, DNAJC30, in 33 unsolved patients from 29 families and establish an autosomal recessive mode of inheritance for LHON (arLHON), which to date has been a prime example of a maternally inherited disorder. Remarkably, all hallmarks of mtLHON were recapitulated, including incomplete penetrance, male predominance, and significant idebenone responsivity. Moreover, by tracking protein turnover in patient-derived cell lines and a DNAJC30-knockout cellular model, we measured reduced turnover of specific complex I N-module subunits and a resultant impairment of complex I function. These results demonstrate that DNAJC30 is a chaperone protein needed for the efficient exchange of complex I subunits exposed to reactive oxygen species and integral to a mitochondrial complex I repair mechanism, thereby providing the first example to our knowledge of a disease resulting from impaired exchange of assembled respiratory chain subunits.
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Affiliation(s)
- Sarah L Stenton
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Natalia L Sheremet
- Federal State Budgetary Institution of Science "Research Institute of Eye Diseases," Moscow, Russia
| | - Claudia B Catarino
- Department of Neurology, Friedrich-Baur-Institute, University Hospital of the Ludwig-Maximilians-Universität München, Munich, Germany
| | - Natalia A Andreeva
- Federal State Budgetary Institution of Science "Research Institute of Eye Diseases," Moscow, Russia
| | - Zahra Assouline
- Fédération de Génétique et Institut Imagine, Université Paris Descartes, Hôpital Necker Enfants Malades, Paris, France
| | | | - Ortal Barel
- Genomics Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Wohl Institute for Translational Medicine, Sheba Medical Center, Tel-Hashomer, Israel
| | - Riccardo Berutti
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Igor Bychkov
- Research Centre for Medical Genetics, Moscow, Russia
| | - Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | | | | | | | - Peter Charbel Issa
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom.,Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Peter Freisinger
- Department of Pediatrics, Klinikum am Steinenberg, Reutlingen, Germany
| | - Sylvie Gerber
- Laboratory Genetics in Ophthalmology (LGO), INSERM UMR1163 - Institute of Genetic Diseases, Imagine. Paris, France
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Elisabeth Graf
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Juliana Heidler
- Functional Proteomics, Medical School, Goethe University, Frankfurt am Main, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Elise Heon
- The Hospital for Sick Children, Department of Ophthalmology and Vision Sciences, The University of Toronto, Toronto, Canada
| | - Yulya S Itkis
- Research Centre for Medical Genetics, Moscow, Russia
| | - Elisheva Javasky
- Genomics Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Wohl Institute for Translational Medicine, Sheba Medical Center, Tel-Hashomer, Israel
| | - Josseline Kaplan
- Laboratory Genetics in Ophthalmology (LGO), INSERM UMR1163 - Institute of Genetic Diseases, Imagine. Paris, France
| | - Robert Kopajtich
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | | | - Reka Kovacs-Nagy
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany.,Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | | | - Wolfram S Kunz
- Department of Experimental Epileptology and Cognition Research, University of Bonn, Bonn, Germany
| | - Chiara La Morgia
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technische Universität München, Munich, Germany
| | - Pedro F Malacarne
- Institute for Cardiovascular Physiology, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | | | - Johannes A Mayr
- Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Jana Meisterknecht
- Functional Proteomics, Medical School, Goethe University, Frankfurt am Main, Germany
| | - Tatiana A Nevinitsyna
- Federal State Budgetary Institution of Science "Research Institute of Eye Diseases," Moscow, Russia
| | - Flavia Palombo
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Ben Pode-Shakked
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Institute for Rare Diseases.,Talpiot Medical Leadership Program, and
| | - Maria S Shmelkova
- Federal State Budgetary Institution of Science "Research Institute of Eye Diseases," Moscow, Russia
| | - Tim M Strom
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany
| | | | - Michal Tzadok
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Amelie T van der Ven
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Matias Wagner
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | | | - Nino V Zhorzholadze
- Federal State Budgetary Institution of Science "Research Institute of Eye Diseases," Moscow, Russia
| | - Jean-Michel Rozet
- Laboratory Genetics in Ophthalmology (LGO), INSERM UMR1163 - Institute of Genetic Diseases, Imagine. Paris, France
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | | | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, University Hospital of the Ludwig-Maximilians-Universität München, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Ilka Wittig
- Functional Proteomics, Medical School, Goethe University, Frankfurt am Main, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
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Allihn PWA, Hackl MW, Ludwig C, Hacker SM, Sieber SA. A tailored phosphoaspartate probe unravels CprR as a response regulator in Pseudomonas aeruginosa interkingdom signaling. Chem Sci 2021; 12:4763-4770. [PMID: 34168754 PMCID: PMC8179651 DOI: 10.1039/d0sc06226j] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/07/2021] [Indexed: 01/06/2023] Open
Abstract
Pseudomonas aeruginosa is a difficult-to-treat Gram-negative bacterial pathogen causing life-threatening infections. Adaptive resistance (AR) to cationic peptide antibiotics such as polymyxin B impairs the therapeutic success. This self-protection is mediated by two component systems (TCSs) consisting of a membrane-bound histidine kinase and an intracellular response regulator (RR). As phosphorylation of the key RR aspartate residue is transient during signaling and hydrolytically unstable, the study of these systems is challenging. Here, we apply a tailored reverse polarity chemical proteomic strategy to capture this transient modification and read-out RR phosphorylation in complex proteomes using a nucleophilic probe. In-depth mechanistic insights into an ideal trapping strategy were performed with a recombinant RR demonstrating the importance of fine-tuned acidic pH values to facilitate the attack on the aspartate carbonyl C-atom and prevent unproductive hydrolysis. Analysis of Bacillus subtilis and P. aeruginosa proteomes revealed the detection of multiple annotated phosphoaspartate (pAsp) sites of known RRs in addition to many new potential pAsp sites. With this validated strategy we dissected the signaling of dynorphin A, a human peptide stress hormone, which is sensed by P. aeruginosa to prepare AR. Intriguingly, our methodology identified CprR as an unprecedented RR in dynorphin A interkingdom signaling.
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Affiliation(s)
- Patrick W A Allihn
- TUM Center for Functional Protein Assemblies (CPA), Department of Chemistry and Chair of Organic Chemistry II, Technical University of Munich Lichtenbergstraße 4 85748 Garching Germany
| | - Mathias W Hackl
- TUM Center for Functional Protein Assemblies (CPA), Department of Chemistry and Chair of Organic Chemistry II, Technical University of Munich Lichtenbergstraße 4 85748 Garching Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich 85354 Freising Germany
| | - Stephan M Hacker
- Department of Chemistry, Technical University of Munich 85748 Garching Germany
| | - Stephan A Sieber
- TUM Center for Functional Protein Assemblies (CPA), Department of Chemistry and Chair of Organic Chemistry II, Technical University of Munich Lichtenbergstraße 4 85748 Garching Germany
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45
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Janßen D, Dworschak L, Ludwig C, Ehrmann MA, Vogel RF. Interspecies assertiveness of Lactobacillus curvatus and Lactobacillus sakei in sausage fermentations. Int J Food Microbiol 2020; 331:108689. [PMID: 32623291 DOI: 10.1016/j.ijfoodmicro.2020.108689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/18/2020] [Accepted: 05/24/2020] [Indexed: 12/25/2022]
Abstract
Lactobacillus (L.) curvatus and L. sakei contain strains, which are assertive in sausage fermentation. Previous work has demonstrated differences in assertiveness at strain level within one species, and revealed either exclusion of competitors by complementary partner strains or their inhibition by single strains. This work addresses interspecies differences in the assertiveness of L. curvatus and L. sakei. Strain sets of L. curvatus and L. sakei were employed as starters in a fermented sausage model and their abundancy upon fermentation was determined by strain-specific MALDI-TOF MS identification. Generally, single or groups of L. sakei strains outcompeted L. curvatus strains. In multiple growth tests employing mMRS and mMSM it could be shown that assertive L. sakei strains can be predicted along their μ max in mMSM. Still, L. curvatus TMW 1.624 could suppress all L. curvatus and most L. sakei strains in competitive settings. This could be referred to its expression of several bacteriocins, which are active against all of the L. curvatus strains. Strain specific differences could be demonstrated in the susceptibility of L. sakei to bacteriocins, and in oxidative stress tolerance, which is higher in co-existing L. sakei strains than in the bacteriocin producer. This suggests that tolerance to bacteriocins and oxidative stress represent additional determinants for assertiveness, above previously reported bacteriocin production versus metabolic complementarism of partner strains.
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Affiliation(s)
- Dorothee Janßen
- Technische Universität München, Lehrstuhl für Technische Mikrobiologie, Freising, Germany
| | - Lena Dworschak
- Technische Universität München, Lehrstuhl für Technische Mikrobiologie, Freising, Germany
| | - Christina Ludwig
- Bayerisches Zentrum für biomolekulare Massenspektrometrie (BayBioMS), Technische Universität München, Freising, Germany
| | - Matthias A Ehrmann
- Technische Universität München, Lehrstuhl für Technische Mikrobiologie, Freising, Germany
| | - Rudi F Vogel
- Technische Universität München, Lehrstuhl für Technische Mikrobiologie, Freising, Germany.
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46
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Nelson CW, Ardern Z, Goldberg TL, Meng C, Kuo CH, Ludwig C, Kolokotronis SO, Wei X. Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic. eLife 2020; 9:e59633. [PMID: 33001029 PMCID: PMC7655111 DOI: 10.7554/elife.59633] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/30/2020] [Indexed: 12/11/2022] Open
Abstract
Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics but are still widely overlooked. We identify and characterize ORF3d, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence of ORF3d translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members of Severe acute respiratory syndrome-related coronavirus), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples). ORF3d has been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as the unrelated gene ORF3b, leading to confusion. Our results liken ORF3d to other accessory genes in emerging viruses and highlight the importance of OLGs.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Viral/immunology
- Antibody Specificity
- Antigens, Viral/biosynthesis
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Betacoronavirus/genetics
- Betacoronavirus/pathogenicity
- Betacoronavirus/physiology
- COVID-19
- China/epidemiology
- Chiroptera/virology
- Coronavirus/genetics
- Coronavirus Infections/epidemiology
- Coronavirus Infections/virology
- Epitopes/genetics
- Epitopes/immunology
- Europe/epidemiology
- Eutheria/virology
- Evolution, Molecular
- Gene Expression Regulation, Viral
- Genes, Overlapping
- Genes, Viral
- Genetic Variation
- Haplotypes/genetics
- Host Specificity/genetics
- Humans
- Models, Molecular
- Mutation
- Open Reading Frames/genetics
- Pandemics
- Phylogeny
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/virology
- Protein Biosynthesis
- Protein Conformation
- RNA, Viral/genetics
- SARS-CoV-2
- Sequence Alignment
- Sequence Homology, Nucleic Acid
- Viral Proteins/genetics
- Viral Proteins/immunology
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Affiliation(s)
- Chase W Nelson
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
- Institute for Comparative Genomics, American Museum of Natural HistoryNew YorkUnited States
| | - Zachary Ardern
- Chair for Microbial Ecology, Technical University of MunichFreisingGermany
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-MadisonMadisonUnited States
- Global Health Institute, University of Wisconsin-MadisonMadisonUnited States
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of MunichFreisingGermany
| | - Chen-Hao Kuo
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of MunichFreisingGermany
| | - Sergios-Orestis Kolokotronis
- Institute for Comparative Genomics, American Museum of Natural HistoryNew YorkUnited States
- Department of Epidemiology and Biostatistics, School of Public Health, SUNY Downstate Health Sciences UniversityBrooklynUnited States
- Institute for Genomic Health, SUNY Downstate Health Sciences UniversityBrooklynUnited States
- Division of Infectious Diseases, Department of Medicine, SUNY Downstate Health Sciences UniversityBrooklynUnited States
| | - Xinzhu Wei
- Departments of Integrative Biology and Statistics, University of California, BerkeleyBerkeleyUnited States
- Departments of Computer Science, Human Genetics, and Computational Medicine, University of California, Los AngelesLos AngelesUnited States
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47
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Zecha J, Lee CY, Bayer FP, Meng C, Grass V, Zerweck J, Schnatbaum K, Michler T, Pichlmair A, Ludwig C, Kuster B. Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing. Mol Cell Proteomics 2020; 19:1503-1522. [PMID: 32591346 PMCID: PMC7780043 DOI: 10.1074/mcp.ra120.002164] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/26/2020] [Indexed: 12/14/2022] Open
Abstract
As the COVID-19 pandemic continues to spread, thousands of scientists around the globe have changed research direction to understand better how the virus works and to find out how it may be tackled. The number of manuscripts on preprint servers is soaring and peer-reviewed publications using MS-based proteomics are beginning to emerge. To facilitate proteomic research on SARS-CoV-2, the virus that causes COVID-19, this report presents deep-scale proteomes (10,000 proteins; >130,000 peptides) of common cell line models, notably Vero E6, Calu-3, Caco-2, and ACE2-A549 that characterize their protein expression profiles including viral entry factors such as ACE2 or TMPRSS2. Using the 9 kDa protein SRP9 and the breast cancer oncogene BRCA1 as examples, we show how the proteome expression data can be used to refine the annotation of protein-coding regions of the African green monkey and the Vero cell line genomes. Monitoring changes of the proteome on viral infection revealed widespread expression changes including transcriptional regulators, protease inhibitors, and proteins involved in innate immunity. Based on a library of 98 stable-isotope labeled synthetic peptides representing 11 SARS-CoV-2 proteins, we developed PRM (parallel reaction monitoring) assays for nano-flow and micro-flow LC-MS/MS. We assessed the merits of these PRM assays using supernatants of virus-infected Vero E6 cells and challenged the assays by analyzing two diagnostic cohorts of 24 (+30) SARS-CoV-2 positive and 28 (+9) negative cases. In light of the results obtained and including recent publications or manuscripts on preprint servers, we critically discuss the merits of MS-based proteomics for SARS-CoV-2 research and testing.
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Affiliation(s)
- Jana Zecha
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Chien-Yun Lee
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Florian P Bayer
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Vincent Grass
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany; German Center for Infection Research (DZIF), Munich partner site, Germany
| | | | | | - Thomas Michler
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Andreas Pichlmair
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany; German Center for Infection Research (DZIF), Munich partner site, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany.
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany; Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany.
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48
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Bechtner J, Ludwig C, Kiening M, Jakob F, Vogel RF. Living the Sweet Life: How Liquorilactobacillus hordei TMW 1.1822 Changes Its Behavior in the Presence of Sucrose in Comparison to Glucose. Foods 2020; 9:foods9091150. [PMID: 32825547 PMCID: PMC7555045 DOI: 10.3390/foods9091150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
Liquorilactobacillus (L.) hordei (formerly Lactobacillus hordei) is one of the dominating lactic acid bacteria within the water kefir consortium, being highly adapted to survive in this environment, while producing high molecular weight dextrans from sucrose. In this work, we extensively studied the physiological response of L. hordei TMW 1.1822 to sucrose compared to glucose, applying label-free, quantitative proteomics of cell lysates and exoproteomes. This revealed the differential expression of 53 proteins within cellular proteomes, mostly associated with carbohydrate uptake and metabolism. Supported by growth experiments, this suggests that L. hordei TMW 1.1822 favors fructose over other sugars. The dextransucrase was expressed irrespectively of the present carbon source, while it was significantly more released in the presence of sucrose (log2FC = 3.09), being among the most abundant proteins within exoproteomes of sucrose-treated cells. Still, L. hordei TMW 1.1822 expressed other sucrose active enzymes, predictively competing with the dextransucrase reaction. While osmolysis appeared to be unlikely, sucrose led to increased release of a multitude of cytoplasmic proteins, suggesting that biofilm formation in L. hordei is not only composed of a polysaccharide matrix but is also of proteinaceous nature. Therefore, our study highlights the intrinsic adaptation of water kefir-borne L. hordei to sucrose-rich habitats and provides fundamental knowledge for its use as a starter culture in plant-based food fermentations with in situ dextran formation.
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Affiliation(s)
- Julia Bechtner
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München (TUM), 85354 Freising, Germany; (J.B.); (F.J.)
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), 85354 Freising, Germany;
| | - Michael Kiening
- Lehrstuhl für Genomorientierte Bioinformatik, Technische Universität München (TUM), 85354 Freising, Germany;
| | - Frank Jakob
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München (TUM), 85354 Freising, Germany; (J.B.); (F.J.)
| | - Rudi F. Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München (TUM), 85354 Freising, Germany; (J.B.); (F.J.)
- Correspondence:
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49
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Lexhaller B, Ludwig C, Scherf KA. Identification of Isopeptides Between Human Tissue Transglutaminase and Wheat, Rye, and Barley Gluten Peptides. Sci Rep 2020; 10:7426. [PMID: 32367038 PMCID: PMC7198585 DOI: 10.1038/s41598-020-64143-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 04/09/2020] [Indexed: 01/28/2023] Open
Abstract
Celiac disease (CD) is a chronic immune-mediated enteropathy of the small intestine, which is triggered by the ingestion of storage proteins (gluten) from wheat, rye, and barley in genetically predisposed individuals. Human tissue transglutaminase (TG2) plays a central role in the pathogenesis of CD, because it is responsible for specific gluten peptide deamidation and covalent crosslinking, resulting in the formation of Nε-(γ-glutamyl)-lysine isopeptide bonds. The resulting TG2-gluten peptide complexes are assumed to cause the secretion of anti-TG2 autoantibodies, but the underlying mechanisms are only partly known. To gain more insight into the structures of these complexes, the aim of our study was to identify TG2-gluten isopeptides. With the use of discovery-driven as well as targeted nanoscale liquid chromatography tandem mass spectrometry, we detected 29 TG2-gluten isopeptides in total, involving seven selected TG2 lysine residues (K205, K265, K429, K468, K590, K600, K677). Several gluten peptides carried known B-cell epitopes and/or T-cell epitopes, either intact 9-mer core regions or partial sequences, as well as sequences bearing striking similarities to already known epitopes. These novel insights into the molecular structures of TG2-gluten peptide complexes may help clarify their physiological relevance in the initiation of CD autoimmunity and the role of anti-TG2 autoantibodies.
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Affiliation(s)
- Barbara Lexhaller
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, 85354, Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Gregor-Mendel-Str. 4, 85354, Freising, Germany
| | - Katharina Anne Scherf
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, 85354, Freising, Germany. .,Department of Bioactive and Functional Food Chemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Adenauerring 20a, 76131, Karlsruhe, Germany.
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50
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Berger JD, Ludwig C, Whisson K. Changing water use and adaptive strategies along rainfall gradients in Mediterranean lupins. Plant Biol (Stuttg) 2020; 22:298-308. [PMID: 31758626 DOI: 10.1111/plb.13076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/25/2019] [Indexed: 06/10/2023]
Abstract
There is growing interest in harnessing the genetic and adaptive diversity of crop wild relatives to improve drought resilience of elite cultivars. Rainfall gradients exert strong selection pressure on both natural and agricultural ecosystems. Understanding plant responses to these facilitates crop improvement. Wild and domesticated narrow-leafed lupin (NLL) collected along Mediterranean terminal drought stress gradients was evaluated under contrasting reproductive phase water supply in controlled field, glasshouse and cabinet studies. Plant phenology, growth and productivity, water use and stress responses were measured over time. There is an integrated suite of adaptive changes along rainfall gradients in NLL. Low rainfall ecotypes flower earlier, accumulate lower seed numbers, biomass and leaf area, and have larger root:shoot ratios than high rainfall ecotypes. Water-use is lower and stress onset slower in low compared to high rainfall ecotypes. Water-use rates and ecotypic differences in stress response (Ψleaf decline, leaf loss) are lower in NLL than yellow lupin (YL). To mitigate the effects of profligate water use, high rainfall YL ecotypes maintain higher leaf water content over declining leaf water potential than low rainfall ecotypes. There is no evidence for such specific adaptation in NLL. The data suggests that appropriate phenology is the key adaptive trait to rainfall gradients in NLL because of the flow-on effects on biomass production, fitness, transpiration and stress onset, and the lack of physiological adaptations as in YL. Accordingly, it is essential to match phenology with target environment in order to minimize risk and maximize yield potential.
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Affiliation(s)
- J D Berger
- CSIRO Agriculture and Food, Wembley, WA, Australia
| | - C Ludwig
- CSIRO Agriculture and Food, Wembley, WA, Australia
| | - K Whisson
- CSIRO Agriculture and Food, Wembley, WA, Australia
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