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Pucelik S, Becker M, Heyber S, Wöhlbrand L, Rabus R, Jahn D, Härtig E. The blue light-dependent LOV-protein LdaP of Dinoroseobacter shibae acts as antirepressor of the PpsR repressor, regulating photosynthetic gene cluster expression. Front Microbiol 2024; 15:1351297. [PMID: 38404597 PMCID: PMC10890935 DOI: 10.3389/fmicb.2024.1351297] [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: 12/06/2023] [Accepted: 01/17/2024] [Indexed: 02/27/2024] Open
Abstract
In the marine α-proteobacterium Dinoroseobacter shibae more than 40 genes of the aerobic anoxygenic photosynthesis are regulated in a light-dependent manner. A genome-wide screen of 5,605 clones from a D. shibae transposon library for loss of pigmentation and changes in bacteriochlorophyll absorbance identified 179 mutant clones. The gene encoding the LOV-domain containing protein Dshi_1135 was identified by its colorless phenotype. The mutant phenotype was complemented by the expression of a Dshi_1135-strep fusion protein in trans. The recombinantly produced and chromatographically purified Dshi_1135 protein was able to undergo a blue light-induced photocycle mediated by bound FMN. Transcriptome analyses revealed an essential role for Dshi_1135 in the light-dependent expression of the photosynthetic gene cluster. Interactomic studies identified the repressor protein PpsR as an interaction partner of Dshi_1135. The physical contact between PpsR and the Dshi_1135 protein was verified in vivo using the bacterial adenylate cyclase-based two-hybrid system. In addition, the antirepressor function of the Dshi_1135 protein was demonstrated in vivo testing of a bchF-lacZ reporter gene fusion in a heterologous Escherichia coli-based host system. We therefore propose to rename the Dshi_1135 protein to LdaP (light-dependent antirepressor of PpsR). Using the bacterial two-hybrid system, it was also shown that cobalamin (B12) is essential for the interaction of the antirepressor PpaA with PpsR. A regulatory model for the photosynthetic gene cluster in D. shibae was derived, including the repressor PpsR, the light-dependent antirepressor LdaP and the B12-dependent antirepressor PpaA.
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Affiliation(s)
- Saskia Pucelik
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Miriam Becker
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Steffi Heyber
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Lars Wöhlbrand
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Elisabeth Härtig
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
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Dougan KE, Deng ZL, Wöhlbrand L, Reuse C, Bunk B, Chen Y, Hartlich J, Hiller K, John U, Kalvelage J, Mansky J, Neumann-Schaal M, Overmann J, Petersen J, Sanchez-Garcia S, Schmidt-Hohagen K, Shah S, Spröer C, Sztajer H, Wang H, Bhattacharya D, Rabus R, Jahn D, Chan CX, Wagner-Döbler I. Multi-omics analysis reveals the molecular response to heat stress in a "red tide" dinoflagellate. Genome Biol 2023; 24:265. [PMID: 37996937 PMCID: PMC10666404 DOI: 10.1186/s13059-023-03107-4] [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: 12/14/2022] [Accepted: 11/10/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND "Red tides" are harmful algal blooms caused by dinoflagellate microalgae that accumulate toxins lethal to other organisms, including humans via consumption of contaminated seafood. These algal blooms are driven by a combination of environmental factors including nutrient enrichment, particularly in warm waters, and are increasingly frequent. The molecular, regulatory, and evolutionary mechanisms that underlie the heat stress response in these harmful bloom-forming algal species remain little understood, due in part to the limited genomic resources from dinoflagellates, complicated by the large sizes of genomes, exhibiting features atypical of eukaryotes. RESULTS We present the de novo assembled genome (~ 4.75 Gbp with 85,849 protein-coding genes), transcriptome, proteome, and metabolome from Prorocentrum cordatum, a globally abundant, bloom-forming dinoflagellate. Using axenic algal cultures, we study the molecular mechanisms that underpin the algal response to heat stress, which is relevant to current ocean warming trends. We present the first evidence of a complementary interplay between RNA editing and exon usage that regulates the expression and functional diversity of biomolecules, reflected by reduction in photosynthesis, central metabolism, and protein synthesis. These results reveal genomic signatures and post-transcriptional regulation for the first time in a pelagic dinoflagellate. CONCLUSIONS Our multi-omics analyses uncover the molecular response to heat stress in an important bloom-forming algal species, which is driven by complex gene structures in a large, high-G+C genome, combined with multi-level transcriptional regulation. The dynamics and interplay of molecular regulatory mechanisms may explain in part how dinoflagellates diversified to become some of the most ecologically successful organisms on Earth.
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Affiliation(s)
- Katherine E Dougan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Zhi-Luo Deng
- Helmholtz-Center for Infection Research (HZI), Inhoffenstraße 7, Braunschweig, 38124, Germany
| | - Lars Wöhlbrand
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, 26129, Oldenburg, Germany
| | - Carsten Reuse
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Boyke Bunk
- German Culture Collection for Microorganisms and Cell Cultures (DSMZ), Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Yibi Chen
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Juliane Hartlich
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Karsten Hiller
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Uwe John
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstraße 231, 26129, Oldenburg, Germany
| | - Jana Kalvelage
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, 26129, Oldenburg, Germany
| | - Johannes Mansky
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Meina Neumann-Schaal
- German Culture Collection for Microorganisms and Cell Cultures (DSMZ), Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Jörg Overmann
- German Culture Collection for Microorganisms and Cell Cultures (DSMZ), Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Jörn Petersen
- German Culture Collection for Microorganisms and Cell Cultures (DSMZ), Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Selene Sanchez-Garcia
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Kerstin Schmidt-Hohagen
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Sarah Shah
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Cathrin Spröer
- German Culture Collection for Microorganisms and Cell Cultures (DSMZ), Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Helena Sztajer
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Hui Wang
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, 26129, Oldenburg, Germany
| | - Dieter Jahn
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Irene Wagner-Döbler
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany.
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Kretschmer M, Müller J, Henke P, Otto V, Rodriguez AA, Müsken M, Jahn D, Borrero-de Acuña JM, Neumann-Schaal M, Wegner A. Isolation and Quantification of Bacterial Membrane Vesicles for Quantitative Metabolic Studies Using Mammalian Cell Cultures. Cells 2023; 12:2674. [PMID: 38067103 PMCID: PMC10705164 DOI: 10.3390/cells12232674] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/10/2023] [Accepted: 11/18/2023] [Indexed: 12/18/2023] Open
Abstract
Bacterial membrane vesicles (BMVs) are produced by most bacteria and participate in various cellular processes, such as intercellular communication, nutrient exchange, and pathogenesis. Notably, these vesicles can contain virulence factors, including toxic proteins, DNA, and RNA. Such factors can contribute to the harmful effects of bacterial pathogens on host cells and tissues. Although the general effects of BMVs on host cellular physiology are well known, the underlying molecular mechanisms are less understood. In this study, we introduce a vesicle quantification method, leveraging the membrane dye FM4-64. We utilize a linear regression model to analyze the fluorescence emitted by stained vesicle membranes to ensure consistent and reproducible vesicle-host interaction studies using cultured cells. This method is particularly valuable for identifying host cellular processes impacted by vesicles and their specific cargo. Moreover, it outcompetes unreliable protein concentration-based methods. We (1) show a linear correlation between the number of vesicles and the fluorescence signal emitted from the FM4-64 dye; (2) introduce the "vesicle load" as a new semi-quantitative unit, facilitating more reproducible vesicle-cell culture interaction experiments; (3) show that a stable vesicle load yields consistent host responses when studying vesicles from Pseudomonas aeruginosa mutants; (4) demonstrate that typical vesicle isolation contaminants, such as flagella, do not significantly skew the metabolic response of lung epithelial cells to P. aeruginosa vesicles; and (5) identify inositol monophosphatase 1 (SuhB) as a pivotal regulator in the vesicle-mediated pathogenesis of P. aeruginosa.
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Affiliation(s)
- Marcel Kretschmer
- Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Julia Müller
- Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Petra Henke
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124 Braunschweig, Germany
| | - Viktoria Otto
- Institute for Microbiology, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | | | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Dieter Jahn
- Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
- Institute for Microbiology, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - José Manuel Borrero-de Acuña
- Department of Microbiology, Facultad de Biología, University of Sevilla, Av. de la Reina Mercedes 6, 41012 Sevilla, Spain
| | - Meina Neumann-Schaal
- Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124 Braunschweig, Germany
| | - Andre Wegner
- Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
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Könemund L, Neumann L, Hirschberg F, Biedendieck R, Jahn D, Johannes HH, Kowalsky W. Author Correction: Functionalization of an extended-gate field-effect transistor (EGFET) for bacteria detection. Sci Rep 2023; 13:19878. [PMID: 37963896 PMCID: PMC10645911 DOI: 10.1038/s41598-023-46380-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023] Open
Affiliation(s)
- Lea Könemund
- Institut für Hochfrequenztechnik, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Laurie Neumann
- Institut für Hochfrequenztechnik, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Felix Hirschberg
- Institut für Hochfrequenztechnik, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Rebekka Biedendieck
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Dieter Jahn
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Hans-Hermann Johannes
- Institut für Hochfrequenztechnik, Technische Universität Braunschweig, 38106, Braunschweig, Germany.
- Cluster of Excellence PhoenixD (Photonics, Optics, and Engineering-Innovation Across Disciplines), 30167, Hannover, Germany.
| | - Wolfgang Kowalsky
- Institut für Hochfrequenztechnik, Technische Universität Braunschweig, 38106, Braunschweig, Germany
- Cluster of Excellence PhoenixD (Photonics, Optics, and Engineering-Innovation Across Disciplines), 30167, Hannover, Germany
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5
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Hamed MM, Abdelsamie AS, Rox K, Schütz C, Kany AM, Röhrig T, Schmelz S, Blankenfeldt W, Arce‐Rodriguez A, Borrero‐de Acuña JM, Jahn D, Rademacher J, Ringshausen FC, Cramer N, Tümmler B, Hirsch AKH, Hartmann RW, Empting M. Towards Translation of PqsR Inverse Agonists: From In Vitro Efficacy Optimization to In Vivo Proof-of-Principle. Adv Sci (Weinh) 2023; 10:e2204443. [PMID: 36596691 PMCID: PMC9929129 DOI: 10.1002/advs.202204443] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/28/2022] [Indexed: 06/17/2023]
Abstract
Pseudomonas aeruginosa (PA) is an opportunistic human pathogen, which is involved in a wide range of dangerous infections. It develops alarming resistances toward antibiotic treatment. Therefore, alternative strategies, which suppress pathogenicity or synergize with antibiotic treatments are in great need to combat these infections more effectively. One promising approach is to disarm the bacteria by interfering with their quorum sensing (QS) system, which regulates the release of various virulence factors as well as biofilm formation. Herein, this work reports the rational design, optimization, and in-depth profiling of a new class of Pseudomonas quinolone signaling receptor (PqsR) inverse agonists. The resulting frontrunner compound features a pyrimidine-based scaffold, high in vitro and in vivo efficacy, favorable pharmacokinetics as well as clean safety pharmacology characteristics, which provide the basis for potential pulmonary as well as systemic routes of administration. An X-ray crystal structure in complex with PqsR facilitated further structure-guided lead optimization. The compound demonstrates potent pyocyanin suppression, synergizes with aminoglycoside antibiotic tobramycin against PA biofilms, and is active against a panel of clinical isolates from bronchiectasis patients. Importantly, this in vitro effect translated into in vivo efficacy in a neutropenic thigh infection model in mice providing a proof-of-principle for adjunctive treatment scenarios.
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Affiliation(s)
- Mostafa M. Hamed
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
| | - Ahmed S. Abdelsamie
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
- Department of Chemistry of Natural and Microbial ProductsInstitute of Pharmaceutical and Drug Industries ResearchNational Research CentreEl‐Buhouth St.DokkiCairo12622Egypt
| | - Katharina Rox
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
- Department of Chemical Biology (CBIO)Helmholtz Centre for Infection Research (HZI)Inhoffenstr. 7 Braunschweig38124SaarbrückenGermany
| | - Christian Schütz
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
| | - Andreas M. Kany
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
| | - Teresa Röhrig
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
| | - Stefan Schmelz
- Department of Structure and Function of Proteins (SFPR)Helmholtz Centre for Infection Research (HZI)Inhoffenstr. 7 Braunschweig38124SaarbrückenGermany
| | - Wulf Blankenfeldt
- Department of Structure and Function of Proteins (SFPR)Helmholtz Centre for Infection Research (HZI)Inhoffenstr. 7 Braunschweig38124SaarbrückenGermany
- Institute for BiochemistryBiotechnology and BioinformaticsTechnische Universität BraunschweigBraunschweigGermany
| | | | - José Manuel Borrero‐de Acuña
- Institute of MicrobiologyTechnische Universität Braunschweig38106BraunschweigGermany
- Braunschweig Integrated Centre of Systems Biology (BRICS)Technische Universität Braunschweig38106BraunschweigGermany
- Departamento de MicrobiologíaFacultad de BiologíaUniversidad de SevillaAv. de la Reina Mercedesno. 6SevillaCP 41012Spain
| | - Dieter Jahn
- Institute of MicrobiologyTechnische Universität Braunschweig38106BraunschweigGermany
- Braunschweig Integrated Centre of Systems Biology (BRICS)Technische Universität Braunschweig38106BraunschweigGermany
| | - Jessica Rademacher
- Department for Respiratory MedicineMedizinische Hochschule HannoverCarl‐Neuberg‐Str. 130625HannoverGermany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH)German Center for Lung Research (DZL)30625HannoverGermany
| | - Felix C. Ringshausen
- Department for Respiratory MedicineMedizinische Hochschule HannoverCarl‐Neuberg‐Str. 130625HannoverGermany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH)German Center for Lung Research (DZL)30625HannoverGermany
- European Reference Network on Rare and Complex Respiratory Diseases (ERN‐ LUNG)FrankfurtGermany
| | - Nina Cramer
- Department for Pediatric PneumologyAllergology and NeonatologyMedizinische Hochschule HannoverCarl‐Neuberg‐Str. 130625HannoverGermany
| | - Burkhard Tümmler
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH)German Center for Lung Research (DZL)30625HannoverGermany
- Department for Pediatric PneumologyAllergology and NeonatologyMedizinische Hochschule HannoverCarl‐Neuberg‐Str. 130625HannoverGermany
| | - Anna K. H. Hirsch
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
- Department of PharmacySaarland University Campus E8.166123SaarbrückenGermany
| | - Rolf W. Hartmann
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
- Department of PharmacySaarland University Campus E8.166123SaarbrückenGermany
| | - Martin Empting
- Helmholtz‐Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) Campus E8.166123SaarbrückenGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐Braunschweig Saarbrücken66123SaarbrückenGermany
- Department of PharmacySaarland University Campus E8.166123SaarbrückenGermany
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Mangan MSJ, Gorki F, Krause K, Heinz A, Pankow A, Ebert T, Jahn D, Hiller K, Hornung V, Maurer M, Schmidt FI, Gerhard R, Latz E. Transcriptional licensing is required for Pyrin inflammasome activation in human macrophages and bypassed by mutations causing familial Mediterranean fever. PLoS Biol 2022; 20:e3001351. [PMID: 36342970 PMCID: PMC9671422 DOI: 10.1371/journal.pbio.3001351] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/17/2022] [Accepted: 09/23/2022] [Indexed: 11/09/2022] Open
Abstract
Pyrin is a cytosolic immune sensor that nucleates an inflammasome in response to inhibition of RhoA by bacterial virulence factors, triggering the release of inflammatory cytokines, including IL-1β. Gain-of-function mutations in the MEFV gene encoding Pyrin cause autoinflammatory disorders, such as familial Mediterranean fever (FMF) and Pyrin-associated autoinflammation with neutrophilic dermatosis (PAAND). To precisely define the role of Pyrin in pathogen detection in human immune cells, we compared initiation and regulation of the Pyrin inflammasome response in monocyte-derived macrophages (hMDM). Unlike human monocytes and murine macrophages, we determined that hMDM failed to activate Pyrin in response to known Pyrin activators Clostridioides difficile (C. difficile) toxins A or B (TcdA or TcdB), as well as the bile acid analogue BAA-473. The Pyrin inflammasome response was enabled in hMDM by prolonged priming with either LPS or type I or II interferons and required an increase in Pyrin expression. Notably, FMF mutations lifted the requirement for prolonged priming for Pyrin activation in hMDM, enabling Pyrin activation in the absence of additional inflammatory signals. Unexpectedly, in the absence of a Pyrin response, we found that TcdB activated the NLRP3 inflammasome in hMDM. These data demonstrate that regulation of Pyrin activation in hMDM diverges from monocytes and highlights its dysregulation in FMF.
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Affiliation(s)
- Matthew S. J. Mangan
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Friederike Gorki
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Karoline Krause
- Institute of Allergology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Allergology and Immunology, Berlin, Germany
| | - Alexander Heinz
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Anne Pankow
- Medizinische Klinik mit Schwerpunkt Rheumatologie und Klinische Immunologie AG Digitale Medizin in der Rheumatologie/ Rheumatologie 4.0 Charité—Universitätsmedizin Berlin (CCM), Berlin, Germany
| | - Thomas Ebert
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dieter Jahn
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marcus Maurer
- Institute of Allergology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Allergology and Immunology, Berlin, Germany
| | - Florian I. Schmidt
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Ralf Gerhard
- Institute of Toxicology, Hannover Medical School, Hannover, Germany
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases, Bonn, Germany
- Department of Infectious Diseases & Immunology, UMass Medical School, Worcester, Massachusetts, United States of America
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway
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7
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Biwer P, Neumann-Schaal M, Henke P, Jahn D, Schulz S. Thiol Metabolism and Volatile Metabolome of Clostridioides difficile. Front Microbiol 2022; 13:864587. [PMID: 35783419 PMCID: PMC9243749 DOI: 10.3389/fmicb.2022.864587] [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: 01/28/2022] [Accepted: 04/22/2022] [Indexed: 11/21/2022] Open
Abstract
Clostridioides difficile (previously Clostridium difficile) causes life-threatening gut infections. The central metabolism of the bacterium is strongly influencing toxin production and consequently the infection progress. In this context, the composition and potential origin of the volatile metabolome was investigated, showing a large number of sulfur-containing volatile metabolites. Gas chromatography/mass spectrometry (GC/MS)-based headspace analyses of growing C. difficile 630Δerm cultures identified 105 mainly sulfur-containing compounds responsible of the typical C. difficile odor. Major components were identified to be 2-methyl-1-propanol, 2-methyl-1-propanethiol, 2-methyl-1-butanethiol, 4-methyl-1-pentanethiol, and as well as their disulfides. Structurally identified were 64 sulfur containing volatiles. In order to determine their biosynthetic origin, the concentrations of the sulfur-containing amino acids methionine and cysteine were varied in the growth medium. The changes observed in the volatile metabolome profile indicated that cysteine plays an essential role in the formation of the sulfur-containing volatiles. We propose that disulfides are derived from cysteine via formation of cystathionine analogs, which lead to corresponding thiols. These thiols may then be oxidized to disulfides. Moreover, methionine may contribute to the formation of short-chain disulfides through integration of methanethiol into the disulfide biosynthesis. In summary, the causative agents of the typical C. difficile odor were identified and first hypotheses for their biosynthesis were proposed.
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Affiliation(s)
- Peter Biwer
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Department of Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology, BRICS, Braunschweig, Germany
| | - Petra Henke
- Department of Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology, BRICS, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
- *Correspondence: Stefan Schulz,
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8
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Abstract
The anaerobic biosyntheses of heme, heme d 1, and bacteriochlorophyll all require the action of radical SAM enzymes. During heme biosynthesis in some bacteria, coproporphyrinogen III dehydrogenase (CgdH) catalyzes the decarboxylation of two propionate side chains of coproporphyrinogen III to the corresponding vinyl groups of protoporphyrinogen IX. Its solved crystal structure was the first published structure for a radical SAM enzyme. In bacteria, heme is inserted into enzymes by the cytoplasmic heme chaperone HemW, a radical SAM enzyme structurally highly related to CgdH. In an alternative heme biosynthesis route found in archaea and sulfate-reducing bacteria, the two radical SAM enzymes AhbC and AhbD catalyze the removal of two acetate groups (AhbC) or the decarboxylation of two propionate side chains (AhbD). NirJ, a close homologue of AhbC, is required for propionate side chain removal during the formation of heme d 1 in some denitrifying bacteria. Biosynthesis of the fifth ring (ring E) of all chlorophylls is based on an unusual six-electron oxidative cyclization step. The sophisticated conversion of Mg-protoporphyrin IX monomethylester to protochlorophyllide is facilitated by an oxygen-independent cyclase termed BchE, which is a cobalamin-dependent radical SAM enzyme. Most of the radical SAM enzymes involved in tetrapyrrole biosynthesis were recognized as such by Sofia et al. in 2001 (Nucleic Acids Res.2001, 29, 1097-1106) and were biochemically characterized thereafter. Although much has been achieved, the challenging tetrapyrrole substrates represent a limiting factor for enzyme/substrate cocrystallization and the ultimate elucidation of the corresponding enzyme mechanisms.
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Affiliation(s)
- Gunhild Layer
- Institut
für Pharmazeutische Wissenschaften, Pharmazeutische Biologie, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Str. 19, 79104 Freiburg im Breisgau, Germany
- . Phone: ++49
0761 203 8373
| | - Martina Jahn
- Institut
für Mikrobiologie, Technische Universität
Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Jürgen Moser
- Institut
für Mikrobiologie, Technische Universität
Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Dieter Jahn
- Braunschweig
Integrated Center of Systems Biology BRICS, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
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9
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Neumann-Schaal M, Groß U, Just I, Jahn D. Editorial: The Deadly Secrets of C. difficile-Insights Into Host-Pathogen Interaction. Front Microbiol 2022; 13:897612. [PMID: 35464954 PMCID: PMC9020219 DOI: 10.3389/fmicb.2022.897612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Meina Neumann-Schaal
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Uwe Groß
- Institute of Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Ingo Just
- Institute of Toxicology, Hannover Medical School, Hanover, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
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10
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Neumann-Schaal M, Groß U, Just I, Jahn D. Editorial: The Deadly Secrets of C. Difficile-Insights Into Host-Pathogen Interaction, Volume II. Front Microbiol 2022; 13:896979. [PMID: 35464962 PMCID: PMC9019597 DOI: 10.3389/fmicb.2022.896979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 11/22/2022] Open
Affiliation(s)
- Meina Neumann-Schaal
- Research Group Metabolomics, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Uwe Groß
- Institute of Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Ingo Just
- Institute of Toxicology, Hannover Medical School, Hannover, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
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11
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Könemund L, Neumann L, Hirschberg F, Biedendieck R, Jahn D, Johannes HH, Kowalsky W. Functionalization of an extended-gate field-effect transistor (EGFET) for bacteria detection. Sci Rep 2022; 12:4397. [PMID: 35292706 PMCID: PMC8924197 DOI: 10.1038/s41598-022-08272-3] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/25/2022] [Indexed: 11/10/2022] Open
Abstract
Traditional sensing technologies have drawbacks as they are time-consuming, cost-intensive, and do not attain the required accuracy and reproducibility. Therefore, new methods of measurements are necessary to improve the detection of bacteria. Well-established electrical measurement methods can connect high sensitive sensing systems with biological requirements. One approach is to functionalize an extended-gate field-effect transistor's (EGFET) sensing area with modified porphyrins containing two different linkers. One linker connects the electrode surface with the porphyrin. The other linker bonds bacteria on the functional layer through a specific peptide chain. The negative charge on the surface of the cells regulates the surface potential which has an impact on the electrical behavior of the EGFET. The attendance of attached bacteria on the functionalized sensing area could successfully be detected.
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Affiliation(s)
- Lea Könemund
- Institut für Hochfrequenztechnik, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Laurie Neumann
- Institut für Hochfrequenztechnik, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Felix Hirschberg
- Institut für Hochfrequenztechnik, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Rebekka Biedendieck
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Dieter Jahn
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Hans-Hermann Johannes
- Institut für Hochfrequenztechnik, Technische Universität Braunschweig, 38106, Braunschweig, Germany.
- Cluster of Excellence PhoenixD (Photonics, Optics, and Engineering-Innovation Across Disciplines), 30167, Hannover, Germany.
| | - Wolfgang Kowalsky
- Institut für Hochfrequenztechnik, Technische Universität Braunschweig, 38106, Braunschweig, Germany
- Cluster of Excellence PhoenixD (Photonics, Optics, and Engineering-Innovation Across Disciplines), 30167, Hannover, Germany
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12
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Michel AM, Borrero-de Acuña JM, Molinari G, Ünal CM, Will S, Derksen E, Barthels S, Bartram W, Schrader M, Rohde M, Zhang H, Hoffmann T, Neumann-Schaal M, Bremer E, Jahn D. Cellular adaptation of Clostridioides difficile to high salinity encompasses a compatible solute-responsive change in cell morphology. Environ Microbiol 2022; 24:1499-1517. [PMID: 35106888 DOI: 10.1111/1462-2920.15925] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/27/2022]
Abstract
Infections by the pathogenic gut bacterium Clostridioides difficile cause severe diarrheas up to a toxic megacolon and are currently among the major causes of lethal bacterial infections. Successful bacterial propagation in the gut is strongly associated with the adaptation to changing nutrition-caused environmental conditions; e.g. environmental salt stresses. Concentrations of 350 mM NaCl, the prevailing salinity in the colon, led to significantly reduced growth of C. difficile. Metabolomics of salt- stressed bacteria revealed a major reduction of the central energy generation pathways, including the Stickland-fermentation reactions. No obvious synthesis of compatible solutes was observed up to 24 h of growth. The ensuing limited tolerance to high salinity and absence of compatible solute synthesis might result from an evolutionary adaptation to the exclusive life of C. difficile in the mammalian gut. Addition of the compatible solutes carnitine, glycine-betaine, γ-butyrobetaine, crotonobetaine, homobetaine, proline-betaine and dimethylsulfoniopropionate (DMSP) restored growth (choline and proline failed) under conditions of high salinity. A bioinformatically-identified OpuF-type ABC-transporter imported most of the used compatible solutes. A long-term adaptation after 48 h included a shift of the Stickland fermentation-based energy metabolism from the utilization to the accumulation of L-proline and resulted in restored growth. Surprisingly, salt stress resulted in the formation of coccoid C. difficile cells instead of the typical rod-shaped cells, a process reverted by the addition of several compatible solutes. Hence, compatible solute import via OpuF is the major immediate adaptation strategy of C. difficile to high salinity-incurred cellular stress. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Annika-Marisa Michel
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - José Manuel Borrero-de Acuña
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Universidad de Sevilla, Facultad de Biología, Departamento de Microbiología, Av. de la Reina Mercedes, n° 6, CP, 41012, Sevilla, Spain
| | - Gabriella Molinari
- Central Facility for Microscopy, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Can Murat Ünal
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Sabine Will
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Elisabeth Derksen
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stefan Barthels
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Wiebke Bartram
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Michel Schrader
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Hao Zhang
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,School of Life Science and Technology, Changchun University of Science and Technology, No. 7186 Weixing Road, 130022, Changchun, China
| | - Tamara Hoffmann
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Meina Neumann-Schaal
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Dieter Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
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13
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Mansky J, Wang H, Ebert M, Härtig E, Jahn D, Tomasch J, Wagner-Döbler I. The Influence of Genes on the “Killer Plasmid” of Dinoroseobacter shibae on Its Symbiosis With the Dinoflagellate Prorocentrum minimum. Front Microbiol 2022; 12:804767. [PMID: 35154034 PMCID: PMC8831719 DOI: 10.3389/fmicb.2021.804767] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 10/29/2021] [Accepted: 12/13/2021] [Indexed: 01/05/2023] Open
Abstract
The marine bacterium Dinoroseobacter shibae shows a Jekyll-and-Hyde behavior in co-culture with the dinoflagellate Prorocentrum minimum: In the initial symbiotic phase it provides the essential vitamins B12 (cobalamin) and B1 (thiamine) to the algae. In the later pathogenic phase it kills the dinoflagellate. The killing phenotype is determined by the 191 kb plasmid and can be conjugated into other Roseobacters. From a transposon-library of D. shibae we retrieved 28 mutants whose insertion sites were located on the 191 kb plasmid. We co-cultivated each of them with P. minimum in L1 medium lacking vitamin B12. With 20 mutant strains no algal growth beyond the axenic control lacking B12 occurred. Several of these genes were predicted to encode proteins from the type IV secretion system (T4SS). They are apparently essential for establishing the symbiosis. With five transposon mutant strains, the initial symbiotic phase was intact but the later pathogenic phase was lost in co-culture. In three of them the insertion sites were located in an operon predicted to encode genes for biotin (B7) uptake. Both P. minimum and D. shibae are auxotrophic for biotin. We hypothesize that the bacterium depletes the medium from biotin resulting in apoptosis of the dinoflagellate.
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Affiliation(s)
- Johannes Mansky
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Hui Wang
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Matthias Ebert
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Elisabeth Härtig
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Dieter Jahn
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Jürgen Tomasch
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Sciences – Centre Algatech, Třeboň, Czechia
| | - Irene Wagner-Döbler
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, Germany
- *Correspondence: Irene Wagner-Döbler,
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14
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Dudek CA, Jahn D. PRODORIC: state-of-the-art database of prokaryotic gene regulation. Nucleic Acids Res 2021; 50:D295-D302. [PMID: 34850133 PMCID: PMC8728284 DOI: 10.1093/nar/gkab1110] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/12/2021] [Accepted: 11/01/2021] [Indexed: 11/14/2022] Open
Abstract
PRODORIC is worldwide one of the largest collections of prokaryotic transcription factor binding sites from multiple bacterial sources with corresponding interpretation and visualization tools. With the introduction of PRODORIC2 in 2017, the transition to a modern web interface and maintainable backend was started. With this latest PRODORIC release the database backend is now fully API-based and provides programmatical access to the complete PRODORIC data. The visualization tools Genome Browser and ProdoNet from the original PRODORIC have been reintroduced and were integrated into the PRODORIC website. Missing input and output options from the original Virtual Footprint were added again for position weight matrix pattern-based searches. The whole PRODORIC dataset was reannotated. Every transcription factor binding site was re-evaluated to increase the overall database quality. During this process, additional parameters, like bound effectors, regulation type and different types of experimental evidence have been added for every transcription factor. Additionally, 109 new transcription factors and 6 new organisms have been added. PRODORIC is publicly available at https://www.prodoric.de.
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Affiliation(s)
- Christian-Alexander Dudek
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, Braunschweig D-38106, Germany
| | - Dieter Jahn
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, Braunschweig D-38106, Germany
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15
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Brauer M, Lassek C, Hinze C, Hoyer J, Becher D, Jahn D, Sievers S, Riedel K. What's a Biofilm?-How the Choice of the Biofilm Model Impacts the Protein Inventory of Clostridioides difficile. Front Microbiol 2021; 12:682111. [PMID: 34177868 PMCID: PMC8225356 DOI: 10.3389/fmicb.2021.682111] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/12/2021] [Indexed: 12/18/2022] Open
Abstract
The anaerobic pathogen Clostridioides difficile is perfectly equipped to survive and persist inside the mammalian intestine. When facing unfavorable conditions C. difficile is able to form highly resistant endospores. Likewise, biofilms are currently discussed as form of persistence. Here a comprehensive proteomics approach was applied to investigate the molecular processes of C. difficile strain 630Δerm underlying biofilm formation. The comparison of the proteome from two different forms of biofilm-like growth, namely aggregate biofilms and colonies on agar plates, revealed major differences in the formation of cell surface proteins, as well as enzymes of its energy and stress metabolism. For instance, while the obtained data suggest that aggregate biofilm cells express both flagella, type IV pili and enzymes required for biosynthesis of cell-surface polysaccharides, the S-layer protein SlpA and most cell wall proteins (CWPs) encoded adjacent to SlpA were detected in significantly lower amounts in aggregate biofilm cells than in colony biofilms. Moreover, the obtained data suggested that aggregate biofilm cells are rather actively growing cells while colony biofilm cells most likely severely suffer from a lack of reductive equivalents what requires induction of the Wood-Ljungdahl pathway and C. difficile’s V-type ATPase to maintain cell homeostasis. In agreement with this, aggregate biofilm cells, in contrast to colony biofilm cells, neither induced toxin nor spore production. Finally, the data revealed that the sigma factor SigL/RpoN and its dependent regulators are noticeably induced in aggregate biofilms suggesting an important role of SigL/RpoN in aggregate biofilm formation.
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Affiliation(s)
- Madita Brauer
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christian Lassek
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christian Hinze
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Juliane Hoyer
- Department for Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Department for Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Susanne Sievers
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
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16
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Beier N, Kucklick M, Fuchs S, Mustafayeva A, Behringer M, Härtig E, Jahn D, Engelmann S. Adaptation of Dinoroseobacter shibae to oxidative stress and the specific role of RirA. PLoS One 2021; 16:e0248865. [PMID: 33780465 PMCID: PMC8007024 DOI: 10.1371/journal.pone.0248865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 03/05/2021] [Indexed: 11/23/2022] Open
Abstract
Dinoroseobacter shibae living in the photic zone of marine ecosystems is frequently exposed to oxygen that forms highly reactive species. Here, we analysed the adaptation of D. shibae to different kinds of oxidative stress using a GeLC-MS/MS approach. D. shibae was grown in artificial seawater medium in the dark with succinate as sole carbon source and exposed to hydrogen peroxide, paraquat or diamide. We quantified 2580 D. shibae proteins. 75 proteins changed significantly in response to peroxide stress, while 220 and 207 proteins were differently regulated by superoxide stress and thiol stress. As expected, proteins like thioredoxin and peroxiredoxin were among these proteins. In addition, proteins involved in bacteriochlophyll biosynthesis were repressed under disulfide and superoxide stress but not under peroxide stress. In contrast, proteins associated with iron transport accumulated in response to peroxide and superoxide stress. Interestingly, the iron-responsive regulator RirA in D. shibae was downregulated by all stressors. A rirA deletion mutant showed an improved adaptation to peroxide stress suggesting that RirA dependent proteins are associated with oxidative stress resistance. Altogether, 139 proteins were upregulated in the mutant strain. Among them are proteins associated with protection and repair of DNA and proteins (e. g. ClpB, Hsp20, RecA, and a thioredoxin like protein). Strikingly, most of the proteins involved in iron metabolism such as iron binding proteins and transporters were not part of the upregulated proteins. In fact, rirA deficient cells were lacking a peroxide dependent induction of these proteins that may also contribute to a higher cell viability under these conditions.
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Affiliation(s)
- Nicole Beier
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
- Microbial Proteomics, Helmholtzzentrum für Infektionsforschung, Braunschweig, Germany
| | - Martin Kucklick
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
- Microbial Proteomics, Helmholtzzentrum für Infektionsforschung, Braunschweig, Germany
| | | | - Ayten Mustafayeva
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
- Microbial Proteomics, Helmholtzzentrum für Infektionsforschung, Braunschweig, Germany
| | - Maren Behringer
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Elisabeth Härtig
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Dieter Jahn
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Susanne Engelmann
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
- Microbial Proteomics, Helmholtzzentrum für Infektionsforschung, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
- * E-mail:
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17
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Chang A, Jeske L, Ulbrich S, Hofmann J, Koblitz J, Schomburg I, Neumann-Schaal M, Jahn D, Schomburg D. BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res 2021; 49:D498-D508. [PMID: 33211880 PMCID: PMC7779020 DOI: 10.1093/nar/gkaa1025] [Citation(s) in RCA: 246] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/14/2020] [Accepted: 10/26/2020] [Indexed: 12/31/2022] Open
Abstract
The BRENDA enzyme database (https://www.brenda-enzymes.org), established in 1987, has evolved into the main collection of functional enzyme and metabolism data. In 2018, BRENDA was selected as an ELIXIR Core Data Resource. BRENDA provides reliable data, continuous curation and updates of classified enzymes, and the integration of newly discovered enzymes. The main part contains >5 million data for ∼90 000 enzymes from ∼13 000 organisms, manually extracted from ∼157 000 primary literature references, combined with information of text and data mining, data integration, and prediction algorithms. Supplements comprise disease-related data, protein sequences, 3D structures, genome annotations, ligand information, taxonomic, bibliographic, and kinetic data. BRENDA offers an easy access to enzyme information from quick to advanced searches, text- and structured-based queries for enzyme-ligand interactions, word maps, and visualization of enzyme data. The BRENDA Pathway Maps are completely revised and updated for an enhanced interactive and intuitive usability. The new design of the Enzyme Summary Page provides an improved access to each individual enzyme. A new protein structure 3D viewer was integrated. The prediction of the intracellular localization of eukaryotic enzymes has been implemented. The new EnzymeDetector combines BRENDA enzyme annotations with protein and genome databases for the detection of eukaryotic and prokaryotic enzymes.
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Affiliation(s)
- Antje Chang
- Technische Universität Braunschweig, Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany
| | - Lisa Jeske
- Technische Universität Braunschweig, Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany
| | - Sandra Ulbrich
- Technische Universität Braunschweig, Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany
| | - Julia Hofmann
- Technische Universität Braunschweig, Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany
| | - Julia Koblitz
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany
| | - Ida Schomburg
- Technische Universität Braunschweig, Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany
| | - Dieter Jahn
- Technische Universität Braunschweig, Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany
| | - Dietmar Schomburg
- Technische Universität Braunschweig, Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany
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18
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Hofmann JD, Biedendieck R, Michel AM, Schomburg D, Jahn D, Neumann-Schaal M. Influence of L-lactate and low glucose concentrations on the metabolism and the toxin formation of Clostridioides difficile. PLoS One 2021; 16:e0244988. [PMID: 33411772 PMCID: PMC7790285 DOI: 10.1371/journal.pone.0244988] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/18/2020] [Indexed: 12/14/2022] Open
Abstract
The virulence of Clostridioides difficile (formerly Clostridium difficile) is mainly caused by its two toxins A and B. Their formation is significantly regulated by metabolic processes. Here we investigated the influence of various sugars (glucose, fructose, mannose, trehalose), sugar derivatives (mannitol and xylitol) and L-lactate on toxin synthesis. Fructose, mannose, trehalose, mannitol and xylitol in the growth medium resulted in an up to 2.2-fold increase of secreted toxin. Low glucose concentration of 2 g/L increased the toxin concentration 1.4-fold compared to growth without glucose, while high glucose concentrations in the growth medium (5 and 10 g/L) led to up to 6.6-fold decrease in toxin formation. Transcriptomic and metabolic investigation of the low glucose effect pointed towards an inactive CcpA and Rex regulatory system. L-lactate (500 mg/L) significantly reduced extracellular toxin formation. Transcriptome analyses of the later process revealed the induction of the lactose utilization operon encoding lactate racemase (larA), electron confurcating lactate dehydrogenase (CDIF630erm_01321) and the corresponding electron transfer flavoprotein (etfAB). Metabolome analyses revealed L-lactate consumption and the formation of pyruvate. The involved electron confurcation process might be responsible for the also observed reduction of the NAD+/NADH ratio which in turn is apparently linked to reduced toxin release from the cell.
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Affiliation(s)
- Julia Danielle Hofmann
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Rebekka Biedendieck
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Annika-Marisa Michel
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- * E-mail:
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19
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Keppler JK, Heyse A, Scheidler E, Uttinger MJ, Fitzner L, Jandt U, Heyn TR, Lautenbach V, Loch JI, Lohr J, Kieserling H, Günther G, Kempf E, Grosch JH, Lewiński K, Jahn D, Lübbert C, Peukert W, Kulozik U, Drusch S, Krull R, Schwarz K, Biedendieck R. Towards recombinantly produced milk proteins: Physicochemical and emulsifying properties of engineered whey protein beta-lactoglobulin variants. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2020.106132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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20
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Massmig M, Reijerse E, Krausze J, Laurich C, Lubitz W, Jahn D, Moser J. Carnitine metabolism in the human gut: characterization of the two-component carnitine monooxygenase CntAB from Acinetobacter baumannii. J Biol Chem 2020; 295:13065-13078. [PMID: 32694223 DOI: 10.1074/jbc.ra120.014266] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/24/2020] [Indexed: 01/29/2023] Open
Abstract
Bacterial formation of trimethylamine (TMA) from carnitine in the gut microbiome has been linked to cardiovascular disease. During this process, the two-component carnitine monooxygenase (CntAB) catalyzes the oxygen-dependent cleavage of carnitine to TMA and malic semialdehyde. Individual redox states of the reductase CntB and the catalytic component CntA were investigated based on mutagenesis and electron paramagnetic resonance (EPR) spectroscopic approaches. Protein ligands of the flavin mononucleotide (FMN) and the plant-type [2Fe-2S] cluster of CntB and also of the Rieske-type [2Fe-2S] cluster and the mononuclear [Fe] center of CntA were identified. EPR spectroscopy of variant CntA proteins suggested a hierarchical metallocenter maturation, Rieske [2Fe-2S] followed by the mononuclear [Fe] center. NADH-dependent electron transfer via the redox components of CntB and within the trimeric CntA complex for the activation of molecular oxygen was investigated. EPR experiments indicated that the two electrons from NADH were allocated to the plant-type [2Fe-2S] cluster and to FMN in the form of a flavin semiquinone radical. Single-turnover experiments of this reduced CntB species indicated the translocation of the first electron onto the [Fe] center and the second electron onto the Rieske-type [2Fe-2S] cluster of CntA to finally allow for oxygen activation as a basis for carnitine cleavage. EPR spectroscopic investigation of CntA variants indicated an unusual intermolecular electron transfer between the subunits of the CntA trimer via the "bridging" residue Glu-205. On the basis of these data, a redox catalytic cycle for carnitine monooxygenase was proposed.
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Affiliation(s)
- Marco Massmig
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | - Edward Reijerse
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Joern Krausze
- Institute of Plant Biology, Technical University Braunschweig, Braunschweig, Germany
| | - Christoph Laurich
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Dieter Jahn
- Braunschweig Centre of Integrated Systems Biology, Braunschweig, Germany
| | - Jürgen Moser
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany.
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21
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Jasper J, Ramos JV, Trncik C, Jahn D, Einsle O, Layer G, Moser J. Chimeric Interaction of Nitrogenase-Like Reductases with the MoFe Protein of Nitrogenase. Chembiochem 2020; 21:1733-1741. [PMID: 31958206 PMCID: PMC7317204 DOI: 10.1002/cbic.201900759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 12/16/2019] [Revised: 01/17/2020] [Indexed: 11/24/2022]
Abstract
The engineering of transgenic organisms with the ability to fix nitrogen is an attractive possibility. However, oxygen sensitivity of nitrogenase, mainly conferred by the reductase component (NifH)2 , is an imminent problem. Nitrogenase-like enzymes involved in coenzyme F430 and chlorophyll biosynthesis utilize the highly homologous reductases (CfbC)2 and (ChlL)2 , respectively. Chimeric protein-protein interactions of these reductases with the catalytic component of nitrogenase (MoFe protein) did not support nitrogenase activity. Nucleotide-dependent association and dissociation of these complexes was investigated, but (CfbC)2 and wild-type (ChlL)2 showed no modulation of the binding affinity. By contrast, the interaction between the (ChlL)2 mutant Y127S and the MoFe protein was markedly increased in the presence of ATP (or ATP analogues) and reduced in the ADP state. Upon formation of the octameric (ChlL)2 MoFe(ChlL)2 complex, the ATPase activity of this variant is triggered, as seen in the homologous nitrogenase system. Thus, the described reductase(s) might be an attractive tool for further elucidation of the diverse functions of (NifH)2 and the rational design of a more robust reductase.
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Affiliation(s)
- Jan Jasper
- Institut für MikrobiologieTechnische Universität BraunschweigSpielmannstrasse 738106BraunschweigGermany
| | - José V. Ramos
- Institut für Pharmazeutische WissenschaftenPharmazeutische Biologie und BiotechnologieAlbert-Ludwigs-Universität FreiburgStefan-Meier-Str. 1979104FreiburgGermany
| | - Christian Trncik
- Institut für BiochemieAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179104FreiburgGermany
| | - Dieter Jahn
- Institut für MikrobiologieTechnische Universität BraunschweigSpielmannstrasse 738106BraunschweigGermany
| | - Oliver Einsle
- Institut für BiochemieAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179104FreiburgGermany
| | - Gunhild Layer
- Institut für Pharmazeutische WissenschaftenPharmazeutische Biologie und BiotechnologieAlbert-Ludwigs-Universität FreiburgStefan-Meier-Str. 1979104FreiburgGermany
| | - Jürgen Moser
- Institut für MikrobiologieTechnische Universität BraunschweigSpielmannstrasse 738106BraunschweigGermany
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22
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Jasper J, Ramos JV, Trncik C, Jahn D, Einsle O, Layer G, Moser J. Front Cover: Chimeric Interaction of Nitrogenase‐Like Reductases with the MoFe Protein of Nitrogenase (ChemBioChem 12/2020). Chembiochem 2020. [DOI: 10.1002/cbic.202000322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jan Jasper
- Institut für Mikrobiologie Technische Universität Braunschweig Spielmannstrasse 7 38106 Braunschweig Germany
| | - José V. Ramos
- Institut für Pharmazeutische Wissenschaften Pharmazeutische Biologie und Biotechnologie Albert-Ludwigs-Universität Freiburg Stefan-Meier-Str. 19 79104 Freiburg Germany
| | - Christian Trncik
- Institut für Biochemie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg Germany
| | - Dieter Jahn
- Institut für Mikrobiologie Technische Universität Braunschweig Spielmannstrasse 7 38106 Braunschweig Germany
| | - Oliver Einsle
- Institut für Biochemie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg Germany
| | - Gunhild Layer
- Institut für Pharmazeutische Wissenschaften Pharmazeutische Biologie und Biotechnologie Albert-Ludwigs-Universität Freiburg Stefan-Meier-Str. 19 79104 Freiburg Germany
| | - Jürgen Moser
- Institut für Mikrobiologie Technische Universität Braunschweig Spielmannstrasse 7 38106 Braunschweig Germany
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23
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Kubannek F, Thiel S, Bunk B, Huber K, Overmann J, Krewer U, Biedendieck R, Jahn D. Performance Modelling of the Bioelectrochemical Glycerol Oxidation by a Co‐Culture of
Geobacter Sulfurreducens
and
Raoultella Electrica. ChemElectroChem 2020. [DOI: 10.1002/celc.202000027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Fabian Kubannek
- Institute of Energy and Process Systems EngineeringTechnische Universität Braunschweig Franz-Liszt-Straße 35 38106 Braunschweig Germany
| | - Simone Thiel
- Institute of Microbiology Braunschweig Integrated Centre of Systems Biology (BRICS)Technische Universität Braunschweig Rebenring 56 38106 Braunschweig Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of MicroorganismsCell Cultures GmbH Inhoffenstraße 7B 38124 Braunschweig Germany
| | - Katharina Huber
- Leibniz Institute DSMZ-German Collection of MicroorganismsCell Cultures GmbH Inhoffenstraße 7B 38124 Braunschweig Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of MicroorganismsCell Cultures GmbH Inhoffenstraße 7B 38124 Braunschweig Germany
| | - Ulrike Krewer
- Institute of Energy and Process Systems EngineeringTechnische Universität Braunschweig Franz-Liszt-Straße 35 38106 Braunschweig Germany
| | - Rebekka Biedendieck
- Institute of Microbiology Braunschweig Integrated Centre of Systems Biology (BRICS)Technische Universität Braunschweig Rebenring 56 38106 Braunschweig Germany
| | - Dieter Jahn
- Institute of Microbiology Braunschweig Integrated Centre of Systems Biology (BRICS)Technische Universität Braunschweig Rebenring 56 38106 Braunschweig Germany
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24
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Eckweiler D, Dudek CA, Hartlich J, Brötje D, Jahn D. PRODORIC2: the bacterial gene regulation database in 2018. Nucleic Acids Res 2019; 46:D320-D326. [PMID: 29136200 PMCID: PMC5753277 DOI: 10.1093/nar/gkx1091] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/21/2017] [Indexed: 12/05/2022] Open
Abstract
Bacteria adapt to changes in their environment via differential gene expression mediated by DNA binding transcriptional regulators. The PRODORIC2 database hosts one of the largest collections of DNA binding sites for prokaryotic transcription factors. It is the result of the thoroughly redesigned PRODORIC database. PRODORIC2 is more intuitive and user-friendly. Besides significant technical improvements, the new update offers more than 1000 new transcription factor binding sites and 110 new position weight matrices for genome-wide pattern searches with the Virtual Footprint tool. Moreover, binding sites deduced from high-throughput experiments were included. Data for 6 new bacterial species including bacteria of the Rhodobacteraceae family were added. Finally, a comprehensive collection of sigma- and transcription factor data for the nosocomial pathogen Clostridium difficile is now part of the database. PRODORIC2 is publicly available at http://www.prodoric2.de.
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Affiliation(s)
- Denitsa Eckweiler
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, Braunschweig D-38106, Germany
| | - Christian-Alexander Dudek
- Department of Bioinformatics and Biochemistry and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, Braunschweig D-38106, Germany
| | - Juliane Hartlich
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, Braunschweig D-38106, Germany
| | - David Brötje
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, Braunschweig D-38106, Germany
| | - Dieter Jahn
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, Braunschweig D-38106, Germany
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25
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Mayer J, Pippel J, Günther G, Müller C, Lauermann A, Knuuti T, Blankenfeldt W, Jahn D, Biedendieck R. Crystal structures and protein engineering of three different penicillin G acylases from Gram-positive bacteria with different thermostability. Appl Microbiol Biotechnol 2019; 103:7537-7552. [PMID: 31227867 DOI: 10.1007/s00253-019-09977-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 02/21/2019] [Revised: 05/16/2019] [Accepted: 06/10/2019] [Indexed: 10/26/2022]
Abstract
Penicillin G acylase (PGA) catalyzes the hydrolysis of penicillin G to 6-aminopenicillanic acid and phenylacetic acid, which provides the precursor for most semisynthetic penicillins. Most applications rely on PGAs from Gram-negative bacteria. Here we describe the first three crystal structures for PGAs from Gram-positive Bacilli and their utilization in protein engineering experiments for the manipulation of their thermostability. PGAs from Bacillus megaterium (BmPGA, Tm = 56.0 °C), Bacillus thermotolerans (BtPGA, Tm = 64.5 °C), and Bacillus sp. FJAT-27231 (FJAT-PGA, Tm = 74.3 °C) were recombinantly produced with B. megaterium, secreted, purified to apparent heterogeneity, and crystallized. Structures with resolutions of 2.20 Å (BmPGA), 2.27 Å (BtPGA), and 1.36 Å (FJAT-PGA) were obtained. They revealed high overall similarity, reflecting the high identity of up to approx. 75%. Notably, the active center displays a deletion of more than ten residues with respect to PGAs from Gram-negatives. This enlarges the substrate binding site and may indicate a different substrate spectrum. Based on the structures, ten single-chain FJAT-PGAs carrying artificial linkers were produced. However, in all cases, complete linker cleavage was observed. While thermostability remained in the wild-type range, the enzymatic activity dropped between 30 and 60%. Furthermore, four hybrid PGAs carrying subunits from two different enzymes were successfully produced. Their thermostabilities mostly lay between the values of the two mother enzymes. For one PGA increased, enzyme activity was observed. Overall, the three novel PGA structures combined with initial protein engineering experiments provide the basis for establishment of new PGA-based biotechnological processes.
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Affiliation(s)
- Janine Mayer
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany
| | - Jan Pippel
- HZI - Helmholtz Centre for Infection Research, Structure and Function of Proteins, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Gabriele Günther
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany
| | - Carolin Müller
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany
| | - Anna Lauermann
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany
| | - Tobias Knuuti
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany
| | - Wulf Blankenfeldt
- HZI - Helmholtz Centre for Infection Research, Structure and Function of Proteins, Inhoffenstraße 7, 38124, Braunschweig, Germany.,Institute of Biotechnology, Biochemistry and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Dieter Jahn
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany
| | - Rebekka Biedendieck
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany.
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26
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Timmis K, Cavicchioli R, Garcia JL, Nogales B, Chavarría M, Stein L, McGenity TJ, Webster N, Singh BK, Handelsman J, de Lorenzo V, Pruzzo C, Timmis J, Martín JLR, Verstraete W, Jetten M, Danchin A, Huang W, Gilbert J, Lal R, Santos H, Lee SY, Sessitsch A, Bonfante P, Gram L, Lin RTP, Ron E, Karahan ZC, van der Meer JR, Artunkal S, Jahn D, Harper L. The urgent need for microbiology literacy in society. Environ Microbiol 2019; 21:1513-1528. [PMID: 30912268 DOI: 10.1111/1462-2920.14611] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 03/24/2019] [Accepted: 03/24/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Kenneth Timmis
- Institute of Microbiology, Technical University Braunschweig, Germany
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| | - José Luis Garcia
- Department of Environmental Biology, Centro de Investigaciones Biológicas (CIB) (CSIC), Madrid, Spain
| | - Balbina Nogales
- Grupo de Microbiologia, Dept. Biologia, Universitat de les Illes Balears, and Instituto Mediterráneo de Estudios Avanzados 8IMEDEA, UIB-CSIC), Palma de Mallorca, Spain
| | - Max Chavarría
- Escuela de Química, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica & Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Lisa Stein
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Terry J McGenity
- School of Biological Sciences, University of Essex, Colchester, UK
| | - Nicole Webster
- Australian Institute of Marine Science, Townsville and Australian Centre for Ecogenomics, University of Queensland, Brisbane, Queensland, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, Australia
| | - Jo Handelsman
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, WI, USA
| | - Victor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnologia, CSIC, Madrid, Spain
| | - Carla Pruzzo
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita (DISTAV), Università degli Studi di Genova, Italy
| | - James Timmis
- Athena Institute, Vrije Universiteit Amsterdam, The Netherlands
| | | | - Willy Verstraete
- Center for Microbial Ecology and Technology (CMET), Ghent University, Belgium
| | - Mike Jetten
- Department of Microbiology, Radboud University Nijmegen, The Netherlands
| | - Antoine Danchin
- Institut Cochin INSERM U1016, CNRS UMR8104, Université Paris Descartes, Paris, France
| | - Wei Huang
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Jack Gilbert
- Dept. of Pediatrics, University of California at San Diego, San Diego, CA, USA
| | - Rup Lal
- Department of Zoology, Molecular Biology Laboratory, University of Delhi, Delhi, India
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Angela Sessitsch
- Bioresources Unit, AIT Austrian Institute of Technology, Tulln, Austria
| | - Paola Bonfante
- Department of Life Science and Systems Biology, University of Torino, Italy
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Raymond T P Lin
- Department of Microbiology and Immunology, National University of Singapore, Singapore
| | - Eliora Ron
- School of Molecular Cell Biology & Biotechnology, Tel Aviv University, Israel
| | - Z Ceren Karahan
- Department of Medical Microbiology, Ankara University, Turkey
| | | | - Seza Artunkal
- Department of Clinical Microbiology, Haydarpaşa Numune Training Hospital, lstanbul, Turkey
| | - Dieter Jahn
- Institute of Microbiology, Technical University Braunschweig, Germany
| | - Lucy Harper
- Society for Applied Microbiology, London, UK
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27
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Ünal CM, Karagöz MS, Berges M, Priebe C, Borrero de Acuña JM, Wissing J, Jänsch L, Jahn D, Steinert M. Pleiotropic Clostridioides difficile Cyclophilin PpiB Controls Cysteine-Tolerance, Toxin Production, the Central Metabolism and Multiple Stress Responses. Front Pharmacol 2019; 10:340. [PMID: 31024308 PMCID: PMC6459899 DOI: 10.3389/fphar.2019.00340] [Citation(s) in RCA: 5] [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: 12/04/2018] [Accepted: 03/19/2019] [Indexed: 01/05/2023] Open
Abstract
The Gram-positive pathogen Clostridioides difficile is the main bacterial agent of nosocomial antibiotic associated diarrhea. Bacterial peptidyl-prolyl-cis/trans-isomerases (PPIases) are well established modulators of virulence that influence the outcome of human pathologies during infections. Here, we present the first interactomic network of the sole cyclophilin-type PPIase of C. difficile (CdPpiB) and show that it has diverse interaction partners including major enzymes of the amino acid-dependent energy (LdhA, EtfAB, Had, Acd) and the glucose-derived (Fba, GapA, Pfo, Pyk, Pyc) central metabolism. Proteins of the general (UspA), oxidative (Rbr1,2,3, Dsr), alkaline (YloU, YphY) and cold shock (CspB) response were found bound to CdPpiB. The transcriptional (Lrp), translational (InfC, RFF) and folding (GroS, DnaK) control proteins were also found attached. For a crucial enzyme of cysteine metabolism, O-acetylserine sulfhydrylase (CysK), the global transcription regulator Lrp and the flagellar subunit FliC, these interactions were independently confirmed using a bacterial two hybrid system. The active site residues F50, F109, and F110 of CdPpiB were shown to be important for the interaction with the residue P87 of Lrp. CysK activity after heat denaturation was restored by interaction with CdPpiB. In accordance, tolerance toward cell wall stress caused by the exposure to amoxicillin was reduced. In the absence of CdPpiB, C. difficile was more susceptible toward L-cysteine. At the same time, the cysteine-mediated suppression of toxin production ceased resulting in higher cytotoxicity. In summary, the cyclophilin-type PPIase of C. difficile (CdPpiB) coordinates major cellular processes via its interaction with major regulators of transcription, translation, protein folding, stress response and the central metabolism.
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Affiliation(s)
- Can Murat Ünal
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Moleküler Biyoteknoloji Bölümü, Türk-Alman Üniversitesi, Istanbul, Turkey
| | | | - Mareike Berges
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany
| | - Christina Priebe
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Josef Wissing
- Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany.,Cellular Proteomics Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lothar Jänsch
- Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany.,Cellular Proteomics Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dieter Jahn
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany.,Helmholtz Centre for Infection Research, Braunschweig, Germany
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28
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Neumann-Schaal M, Jahn D, Schmidt-Hohagen K. Metabolism the Difficile Way: The Key to the Success of the Pathogen Clostridioides difficile. Front Microbiol 2019; 10:219. [PMID: 30828322 PMCID: PMC6384274 DOI: 10.3389/fmicb.2019.00219] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [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: 09/28/2018] [Accepted: 01/28/2019] [Indexed: 12/11/2022] Open
Abstract
Strains of Clostridioides difficile cause detrimental diarrheas with thousands of deaths worldwide. The infection process by the Gram-positive, strictly anaerobic gut bacterium is directly related to its unique metabolism, using multiple Stickland-type amino acid fermentation reactions coupled to Rnf complex-mediated sodium/proton gradient formation for ATP generation. Major pathways utilize phenylalanine, leucine, glycine and proline with the formation of 3-phenylproprionate, isocaproate, butyrate, 5-methylcaproate, valerate and 5-aminovalerate. In parallel a versatile sugar catabolism including pyruvate formate-lyase as a central enzyme and an incomplete tricarboxylic acid cycle to prevent unnecessary NADH formation completes the picture. However, a complex gene regulatory network that carefully mediates the continuous adaptation of this metabolism to changing environmental conditions is only partially elucidated. It involves the pleiotropic regulators CodY and SigH, the known carbon metabolism regulator CcpA, the proline regulator PrdR, the iron regulator Fur, the small regulatory RNA CsrA and potentially the NADH-responsive regulator Rex. Here, we describe the current knowledge of the metabolic principles of energy generation by C. difficile and the underlying gene regulatory scenarios.
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Affiliation(s)
- Meina Neumann-Schaal
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Integrated Centre of Systems Biology (BRICS), Braunschweig University of Technology, Braunschweig, Germany
| | - Dieter Jahn
- Integrated Centre of Systems Biology (BRICS), Braunschweig University of Technology, Braunschweig, Germany.,Institute of Microbiology, Braunschweig University of Technology, Braunschweig, Germany
| | - Kerstin Schmidt-Hohagen
- Integrated Centre of Systems Biology (BRICS), Braunschweig University of Technology, Braunschweig, Germany.,Department of Bioinformatics and Biochemistry, Braunschweig University of Technology, Braunschweig, Germany
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29
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Blaženović I, Kind T, Sa MR, Ji J, Vaniya A, Wancewicz B, Roberts BS, Torbašinović H, Lee T, Mehta SS, Showalter MR, Song H, Kwok J, Jahn D, Kim J, Fiehn O. Structure Annotation of All Mass Spectra in Untargeted Metabolomics. Anal Chem 2019; 91:2155-2162. [PMID: 30608141 DOI: 10.1021/acs.analchem.8b04698] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ivana Blaženović
- West Coast Metabolomics Center, University of California, Davis, Davis, California 95616, United States
| | - Tobias Kind
- West Coast Metabolomics Center, University of California, Davis, Davis, California 95616, United States
| | - Michael R. Sa
- West Coast Metabolomics Center, University of California, Davis, Davis, California 95616, United States
| | - Jian Ji
- School of Food Science, State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 330047, China
| | - Arpana Vaniya
- West Coast Metabolomics Center, University of California, Davis, Davis, California 95616, United States
| | - Benjamin Wancewicz
- West Coast Metabolomics Center, University of California, Davis, Davis, California 95616, United States
| | - Bryan S. Roberts
- West Coast Metabolomics Center, University of California, Davis, Davis, California 95616, United States
| | | | - Tack Lee
- Department of Urology, Inha University College of Medicine, Incheon 22212, South Korea
| | - Sajjan S. Mehta
- West Coast Metabolomics Center, University of California, Davis, Davis, California 95616, United States
| | - Megan R. Showalter
- West Coast Metabolomics Center, University of California, Davis, Davis, California 95616, United States
| | - Hosook Song
- Department of Urology, Inha University College of Medicine, Incheon 22212, South Korea
| | - Jessica Kwok
- West Coast Metabolomics Center, University of California, Davis, Davis, California 95616, United States
| | - Dieter Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig 38106, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig 38106, Germany
| | - Jayoung Kim
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
- Department of Medicine, University of California Los Angeles, Los Angeles, California 90095, United States
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
- Department of Urology, Ga Cheon University College of Medicine, Incheon 22212, South Korea
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, Davis, California 95616, United States
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30
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Berges M, Michel AM, Lassek C, Nuss AM, Beckstette M, Dersch P, Riedel K, Sievers S, Becher D, Otto A, Maaß S, Rohde M, Eckweiler D, Borrero-de Acuña JM, Jahn M, Neumann-Schaal M, Jahn D. Iron Regulation in Clostridioides difficile. Front Microbiol 2018; 9:3183. [PMID: 30619231 PMCID: PMC6311696 DOI: 10.3389/fmicb.2018.03183] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [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: 09/24/2018] [Accepted: 12/10/2018] [Indexed: 12/13/2022] Open
Abstract
The response to iron limitation of several bacteria is regulated by the ferric uptake regulator (Fur). The Fur-regulated transcriptional, translational and metabolic networks of the Gram-positive, pathogen Clostridioides difficile were investigated by a combined RNA sequencing, proteomic, metabolomic and electron microscopy approach. At high iron conditions (15 μM) the C. difficile fur mutant displayed a growth deficiency compared to wild type C. difficile cells. Several iron and siderophore transporter genes were induced by Fur during low iron (0.2 μM) conditions. The major adaptation to low iron conditions was observed for the central energy metabolism. Most ferredoxin-dependent amino acid fermentations were significantly down regulated (had, etf, acd, grd, trx, bdc, hbd). The substrates of these pathways phenylalanine, leucine, glycine and some intermediates (phenylpyruvate, 2-oxo-isocaproate, 3-hydroxy-butyryl-CoA, crotonyl-CoA) accumulated, while end products like isocaproate and butyrate were found reduced. Flavodoxin (fldX) formation and riboflavin biosynthesis (rib) were enhanced, most likely to replace the missing ferredoxins. Proline reductase (prd), the corresponding ion pumping RNF complex (rnf) and the reaction product 5-aminovalerate were significantly enhanced. An ATP forming ATPase (atpCDGAHFEB) of the F0F1-type was induced while the formation of a ATP-consuming, proton-pumping V-type ATPase (atpDBAFCEKI) was decreased. The [Fe-S] enzyme-dependent pyruvate formate lyase (pfl), formate dehydrogenase (fdh) and hydrogenase (hyd) branch of glucose utilization and glycogen biosynthesis (glg) were significantly reduced, leading to an accumulation of glucose and pyruvate. The formation of [Fe-S] enzyme carbon monoxide dehydrogenase (coo) was inhibited. The fur mutant showed an increased sensitivity to vancomycin and polymyxin B. An intensive remodeling of the cell wall was observed, Polyamine biosynthesis (spe) was induced leading to an accumulation of spermine, spermidine, and putrescine. The fur mutant lost most of its flagella and motility. Finally, the CRISPR/Cas and a prophage encoding operon were downregulated. Fur binding sites were found upstream of around 20 of the regulated genes. Overall, adaptation to low iron conditions in C. difficile focused on an increase of iron import, a significant replacement of iron requiring metabolic pathways and the restructuring of the cell surface for protection during the complex adaptation phase and was only partly directly regulated by Fur.
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Affiliation(s)
- Mareike Berges
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Annika-Marisa Michel
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Christian Lassek
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Aaron M Nuss
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Michael Beckstette
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Katharina Riedel
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Susanne Sievers
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Andreas Otto
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Sandra Maaß
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Denitsa Eckweiler
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Martina Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
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31
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Ünal CM, Berges M, Smit N, Schiene-Fischer C, Priebe C, Strowig T, Jahn D, Steinert M. PrsA2 (CD630_35000) of Clostridioides difficile Is an Active Parvulin-Type PPIase and a Virulence Modulator. Front Microbiol 2018; 9:2913. [PMID: 30564207 PMCID: PMC6288519 DOI: 10.3389/fmicb.2018.02913] [Citation(s) in RCA: 6] [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: 05/17/2018] [Accepted: 11/13/2018] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile is the main cause for nosocomial antibiotic associated diarrhea and has become a major burden for the health care systems of industrial countries. Its main virulence factors, the small GTPase glycosylating toxins TcdA and TcdB, are extensively studied. In contrast, the contribution of other factors to development and progression of C. difficile infection (CDI) are only insufficiently understood. Many bacterial peptidyl-prolyl-cis/trans-isomerases (PPIases) have been described in the context of virulence. Among them are the parvulin-type PrsA-like PPIases of Gram-positive bacteria. On this basis, we identified CD630_35000 as the PrsA2 homolog in C. difficile and conducted its enzymatic and phenotypic characterization in order to assess its involvement during C. difficile infection. For this purpose, wild type CdPrsA2 and mutant variants carrying amino acid exchanges mainly in the PPIase domain were recombinantly produced. Recombinant CdPrsA2 showed PPIase activity toward the substrate peptide Ala-Xaa-Pro-Phe with a preference for positively charged amino acids preceding the proline residue. Mutation of conserved residues in its active site pocket impaired the enzymatic activity. A PrsA2 deficient mutant was generated in the C. difficile 630Δerm background using the ClosTron technology. Inactivation of prsA2 resulted in a reduced germination rate in response to taurocholic acid, and in a slight increase in resistance to the secondary bile acids LCA and DCA. Interestingly, in the absence of PrsA2 colonization of mice by C. difficile 630 was significantly reduced. We concluded that CdPrsA2 is an active PPIase that acts as a virulence modulator by influencing crucial processes like sporulation, germination and bile acid resistance resulting in attenuated mice colonization.
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Affiliation(s)
- Can Murat Ünal
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Türk-Alman Üniversitesi, Moleküler Biyoteknoloji Bölümü, Istanbul, Turkey
| | - Mareike Berges
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nathiana Smit
- Helmholtz-Zentrum für Infektionsforschung, Braunschweig, Germany
| | - Cordelia Schiene-Fischer
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Christina Priebe
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Till Strowig
- Helmholtz-Zentrum für Infektionsforschung, Braunschweig, Germany
| | - Dieter Jahn
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Helmholtz-Zentrum für Infektionsforschung, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany
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32
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Groenewold MK, Hebecker S, Fritz C, Czolkoss S, Wiesselmann M, Heinz DW, Jahn D, Narberhaus F, Aktas M, Moser J. Virulence of Agrobacterium tumefaciens requires lipid homeostasis mediated by the lysyl-phosphatidylglycerol hydrolase AcvB. Mol Microbiol 2018; 111:269-286. [PMID: 30353924 DOI: 10.1111/mmi.14154] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2018] [Indexed: 12/24/2022]
Abstract
Agrobacterium tumefaciens transfers oncogenic T-DNA via the type IV secretion system (T4SS) into plants causing tumor formation. The acvB gene encodes a virulence factor of unknown function required for plant transformation. Here we specify AcvB as a periplasmic lysyl-phosphatidylglycerol (L-PG) hydrolase, which modulates L-PG homeostasis. Through functional characterization of recombinant AcvB variants, we showed that the C-terminal domain of AcvB (residues 232-456) is sufficient for full enzymatic activity and defined key residues for catalysis. Absence of the hydrolase resulted in ~10-fold increase in L-PG in Agrobacterium membranes and abolished T-DNA transfer and tumor formation. Overproduction of the L-PG synthase gene (lpiA) in wild-type A. tumefaciens resulted in a similar increase in the L-PG content (~7-fold) and a virulence defect even in the presence of intact AcvB. These results suggest that elevated L-PG amounts (either by overproduction of the synthase or absence of the hydrolase) are responsible for the virulence phenotype. Gradually increasing the L-PG content by complementation with different acvB variants revealed that cellular L-PG levels above 3% of total phospholipids interfere with T-DNA transfer. Cumulatively, this study identified AcvB as a novel virulence factor required for membrane lipid homeostasis and T-DNA transfer.
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Affiliation(s)
- Maike K Groenewold
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Stefanie Hebecker
- Institute for Microbiology, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Christiane Fritz
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Simon Czolkoss
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Milan Wiesselmann
- Institute for Microbiology, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Dirk W Heinz
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Dieter Jahn
- Institute for Microbiology, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Franz Narberhaus
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Meriyem Aktas
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Jürgen Moser
- Institute for Microbiology, Technische Universität Braunschweig, 38106, Braunschweig, Germany
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33
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Bernal I, Hofmann JD, Bulitta B, Klawonn F, Michel AM, Jahn D, Neumann-Schaal M, Bruder D, Jänsch L. Clostridioides difficile Activates Human Mucosal-Associated Invariant T Cells. Front Microbiol 2018; 9:2532. [PMID: 30410474 PMCID: PMC6209678 DOI: 10.3389/fmicb.2018.02532] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/04/2018] [Indexed: 12/13/2022] Open
Abstract
Clostridioides difficile infection (CDI) causes severe inflammatory responses at the intestinal mucosa but the immunological mechanisms underlying CDI-related immunopathology are still incompletely characterized. Here we identified for the first time that both, non-toxigenic strains as well as the hypervirulent ribotypes RT027 and RT023 of Clostridioides difficile (formerly Clostridium difficile), induced an effector phenotype in mucosal-associated invariant T (MAIT) cells. MAIT cells can directly respond to bacterial infections by recognizing MR1-presented metabolites derived from the riboflavin synthesis pathway constituting a novel class of antigens. We confirmed functional riboflavin synthesis of C. difficile and found fixed bacteria capable of activating primary human MAIT cells in a dose-dependent manner. C. difficile-activated MAIT cells showed an increased and MR1-dependent expression of CD69, proinflammatory IFNγ, and the lytic granule components granzyme B and perforin. Effector protein expression was accompanied by the release of lytic granules, which, in contrast to other effector functions, was mainly induced by IL-12 and IL-18. Notably, this study revealed hypervirulent C. difficile strains to be most competent in provoking MAIT cell responses suggesting MAIT cell activation to be instrumental for the immunopathology observed in C. difficile-associated colitis. In conclusion, we provide first evidence for a link between C. difficile metabolism and innate T cell-mediated immunity in humans.
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Affiliation(s)
- Isabel Bernal
- Institute of Medical Microbiology and Hospital Hygiene, Infection Immunology, Otto von Guericke University Magdeburg, Magdeburg, Germany.,Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany.,ESF Graduate School ABINEP, Magdeburg, Germany
| | - Julia Danielle Hofmann
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology, Technical University of Braunschweig, Braunschweig, Germany
| | | | - Frank Klawonn
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Department of Computer Science, Ostfalia University of Applied Sciences, Wolfenbüttel, Germany
| | - Annika-Marisa Michel
- Department of Microbiology, Braunschweig Integrated Centre of Systems Biology, Technical University of Braunschweig, Braunschweig, Germany
| | - Dieter Jahn
- Department of Microbiology, Braunschweig Integrated Centre of Systems Biology, Technical University of Braunschweig, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology, Technical University of Braunschweig, Braunschweig, Germany.,Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dunja Bruder
- Institute of Medical Microbiology and Hospital Hygiene, Infection Immunology, Otto von Guericke University Magdeburg, Magdeburg, Germany.,Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lothar Jänsch
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
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34
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Härtig E, Frädrich C, Behringer M, Hartmann A, Neumann‐Schaal M, Jahn D. Functional definition of the two effector binding sites, the oligomerization and DNA binding domains of the
Bacillus subtilis
LysR‐type transcriptional regulator AlsR. Mol Microbiol 2018; 109:845-864. [DOI: 10.1111/mmi.14089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 07/19/2018] [Accepted: 07/21/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Elisabeth Härtig
- Institute of Microbiology Technische Universität Braunschweig Braunschweig D‐38106Germany
| | - Claudia Frädrich
- Institute of Microbiology Technische Universität Braunschweig Braunschweig D‐38106Germany
| | - Maren Behringer
- Institute of Microbiology Technische Universität Braunschweig Braunschweig D‐38106Germany
| | - Anja Hartmann
- Institute of Microbiology Technische Universität Braunschweig Braunschweig D‐38106Germany
| | - Meina Neumann‐Schaal
- Department of Bioinformatics & Biochemistry Technische Universität Braunschweig Braunschweig D‐38106Germany
| | - Dieter Jahn
- Institute of Microbiology Technische Universität Braunschweig Braunschweig D‐38106Germany
- Braunschweig Integrated Center of Systems Biology (BRICS) Braunschweig D‐38106Germany
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35
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Jahn D, Träger M, Kis M, Brabetz C, Schumacher D, Blažević A, Ciobanu M, Pomorski M, Bonnes U, Busold S, Kroll F, Brack FE, Schramm U, Roth M. Chemical-vapor deposited ultra-fast diamond detectors for temporal measurements of ion bunches. Rev Sci Instrum 2018; 89:093304. [PMID: 30278706 DOI: 10.1063/1.5048667] [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] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/09/2018] [Indexed: 06/08/2023]
Abstract
This article reports on the development of thin diamond detectors and their characterization for their application in temporal profile measurements of subnanosecond ion bunches. Two types of diamonds were used: a 20 μm thin polycrystalline chemical vapor deposited (CVD) diamond and a membrane with a thickness of (5 ± 1) μm etched out of a single crystal (sc) CVD diamond. The combination of a small detector electrode and an impedance matched signal outlet leads to excellent time response properties with a signal pulse resolution (FWHM) of τ = (113 ± 11) ps. Such a fast diamond detector is a perfect device for the time of flight measurements of MeV ions with bunch durations in the subnanosecond regime. The scCVD diamond membrane detector was successfully implemented within the framework of the laser ion generation handling and transport project, in which ion beams are accelerated via a laser-driven source and shaped with conventional accelerator technology. The detector was used to measure subnanosecond proton bunches with an intensity of 108 protons per bunch.
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Affiliation(s)
- D Jahn
- Institut für Kernphysik, Technische Universität Darmstadt, Schloßgartenstraße 9, D-64289 Darmstadt, Germany
| | - M Träger
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - M Kis
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - C Brabetz
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - D Schumacher
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - A Blažević
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - M Ciobanu
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - M Pomorski
- CEA-LIST, Diamond Sensors Laboratory, Gif-sur-Yvette F-91191, France
| | - U Bonnes
- Institut für Kernphysik, Technische Universität Darmstadt, Schloßgartenstraße 9, D-64289 Darmstadt, Germany
| | - S Busold
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - F Kroll
- Technische Universität Dresden, Mommsenstr. 13, 01069 Dresden, Germany
| | - F-E Brack
- Technische Universität Dresden, Mommsenstr. 13, 01069 Dresden, Germany
| | - U Schramm
- Technische Universität Dresden, Mommsenstr. 13, 01069 Dresden, Germany
| | - M Roth
- Institut für Kernphysik, Technische Universität Darmstadt, Schloßgartenstraße 9, D-64289 Darmstadt, Germany
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36
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Hofmann JD, Otto A, Berges M, Biedendieck R, Michel AM, Becher D, Jahn D, Neumann-Schaal M. Metabolic Reprogramming of Clostridioides difficile During the Stationary Phase With the Induction of Toxin Production. Front Microbiol 2018; 9:1970. [PMID: 30186274 PMCID: PMC6110889 DOI: 10.3389/fmicb.2018.01970] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [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: 06/01/2018] [Accepted: 08/03/2018] [Indexed: 12/20/2022] Open
Abstract
The obligate anaerobe, spore forming bacterium Clostridioides difficile (formerly Clostridium difficile) causes nosocomial and community acquired diarrhea often associated with antibiotic therapy. Major virulence factors of the bacterium are the two large clostridial toxins TcdA and TcdB. The production of both toxins was found strongly connected to the metabolism and the nutritional status of the growth environment. Here, we systematically investigated the changes of the gene regulatory, proteomic and metabolic networks of C. difficile 630Δerm underlying the adaptation to the non-growing state in the stationary phase. Integrated data from time-resolved transcriptome, proteome and metabolome investigations performed under defined growth conditions uncovered multiple adaptation strategies. Overall changes in the cellular processes included the downregulation of ribosome production, lipid metabolism, cold shock proteins, spermine biosynthesis, and glycolysis and in the later stages of riboflavin and coenzyme A (CoA) biosynthesis. In contrast, different chaperones, several fermentation pathways, and cysteine, serine, and pantothenate biosynthesis were found upregulated. Focusing on the Stickland amino acid fermentation and the central carbon metabolism, we discovered the ability of C. difficile to replenish its favored amino acid cysteine by a pathway starting from the glycolytic 3-phosphoglycerate via L-serine as intermediate. Following the growth course, the reductive equivalent pathways used were sequentially shifted from proline via leucine/phenylalanine to the central carbon metabolism first to butanoate fermentation and then further to lactate fermentation. The toxin production was found correlated mainly to fluxes of the central carbon metabolism. Toxin formation in the supernatant was detected when the flux changed from butanoate to lactate synthesis in the late stationary phase. The holistic view derived from the combination of transcriptome, proteome and metabolome data allowed us to uncover the major metabolic strategies that are used by the clostridial cells to maintain its cellular homeostasis and ensure survival under starvation conditions.
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Affiliation(s)
- Julia D Hofmann
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Andreas Otto
- Department for Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | - Mareike Berges
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Rebekka Biedendieck
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Annika-Marisa Michel
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Dörte Becher
- Department for Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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37
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Kirchhoff C, Ebert M, Jahn D, Cypionka H. Chemiosmotic Energy Conservation in Dinoroseobacter shibae: Proton Translocation Driven by Aerobic Respiration, Denitrification, and Photosynthetic Light Reaction. Front Microbiol 2018; 9:903. [PMID: 29867814 PMCID: PMC5954134 DOI: 10.3389/fmicb.2018.00903] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/18/2018] [Indexed: 11/13/2022] Open
Abstract
Dinoroseobacter shibae is an aerobic anoxygenic phototroph and able to utilize light energy to support its aerobic energy metabolism. Since the cells can also grow anaerobically with nitrate and nitrite as terminal electron acceptor, we were interested in how the cells profit from photosynthesis during denitrification and what the steps of chemiosmotic energy conservation are. Therefore, we conducted proton translocation experiments and compared O2-, NO3-, and NO2- respiration during different light regimes and in the dark. We used wild type cells and transposon mutants with knocked-out nitrate- and nitrite- reductase genes (napA and nirS), as well as a mutant (ppsR) impaired in bacteriochlorophyll a synthesis. Light had a positive impact on proton translocation, independent of the type of terminal electron acceptor present. In the absence of an electron acceptor, however, light did not stimulate proton translocation. The light-driven add-on to proton translocation was about 1.4 H+/e- for O2 respiration and about 1.1 H+/e- for NO3- and NO2-. We could see that the chemiosmotic energy conservation during aerobic respiration involved proton translocation, mediated by the NADH dehydrogenase, the cytochrome bc1 complex, and the cytochrome c oxidase. During denitrification the last proton translocation step of the electron transport was missing, resulting in a lower H+/e- ratio during anoxia. Furthermore, we studied the type of light-harvesting and found that the cells were able to channel light from the green–blue spectrum most efficiently, while red light has only minor impact. This fits well with the depth profiles for D. shibae abundance in the ocean and the penetration depth of light with different wavelengths into the water column.
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Affiliation(s)
- Christian Kirchhoff
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Matthias Ebert
- Institute of Microbiology, Braunschweig University of Technology, Braunschweig, Germany
| | - Dieter Jahn
- Institute of Microbiology, Braunschweig University of Technology, Braunschweig, Germany
| | - Heribert Cypionka
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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38
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Haskamp V, Karrie S, Mingers T, Barthels S, Alberge F, Magalon A, Müller K, Bill E, Lubitz W, Kleeberg K, Schweyen P, Bröring M, Jahn M, Jahn D. The radical SAM protein HemW is a heme chaperone. J Biol Chem 2018; 293:2558-2572. [PMID: 29282292 PMCID: PMC5818191 DOI: 10.1074/jbc.ra117.000229] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 10/25/2017] [Revised: 12/14/2017] [Indexed: 11/06/2022] Open
Abstract
Radical S-adenosylmethionine (SAM) enzymes exist in organisms from all kingdoms of life, and all of these proteins generate an adenosyl radical via the homolytic cleavage of the S-C(5') bond of SAM. Of particular interest are radical SAM enzymes, such as heme chaperones, that insert heme into respiratory enzymes. For example, heme chaperones insert heme into target proteins but have been studied only for the formation of cytochrome c-type hemoproteins. Here, we report that a radical SAM protein, the heme chaperone HemW from bacteria, is required for the insertion of heme b into respiratory chain enzymes. As other radical SAM proteins, HemW contains three cysteines and one SAM coordinating an [4Fe-4S] cluster, and we observed one heme per subunit of HemW. We found that an intact iron-sulfur cluster was required for HemW dimerization and HemW-catalyzed heme transfer but not for stable heme binding. A bacterial two-hybrid system screen identified bacterioferritins and the heme-containing subunit NarI of the respiratory nitrate reductase NarGHI as proteins that interact with HemW. We also noted that the bacterioferritins potentially serve as heme donors for HemW. Of note, heme that was covalently bound to HemW was actively transferred to a heme-depleted, catalytically inactive nitrate reductase, restoring its nitrate-reducing enzyme activity. Finally, the human HemW orthologue radical SAM domain-containing 1 (RSAD1) stably bound heme. In conclusion, our findings indicate that the radical SAM protein family HemW/RSAD1 is a heme chaperone catalyzing the insertion of heme into hemoproteins.
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Affiliation(s)
| | | | | | | | - François Alberge
- Laboratoire de Chimie Bactérienne UMR7283, CNRS, Aix-Marseille Université, 13009 Marseille, France, and
| | - Axel Magalon
- Laboratoire de Chimie Bactérienne UMR7283, CNRS, Aix-Marseille Université, 13009 Marseille, France, and
| | | | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
| | | | | | | | | | - Dieter Jahn
- Braunschweig Centre of Integrated Systems Biology (BRICS), University Braunschweig, D-38106 Braunschweig, Germany,
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39
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Borrero-de Acuña JM, Timmis KN, Jahn M, Jahn D. Protein complex formation during denitrification by Pseudomonas aeruginosa. Microb Biotechnol 2017; 10:1523-1534. [PMID: 28857512 PMCID: PMC5658584 DOI: 10.1111/1751-7915.12851] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 06/20/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/18/2022] Open
Abstract
The most efficient means of generating cellular energy is through aerobic respiration. Under anaerobic conditions, several prokaryotes can replace oxygen by nitrate as final electron acceptor. During denitrification, nitrate is reduced via nitrite, NO and N2O to molecular nitrogen (N2) by four membrane‐localized reductases with the simultaneous formation of an ion gradient for ATP synthesis. These four multisubunit enzyme complexes are coupled in four electron transport chains to electron donating primary dehydrogenases and intermediate electron transfer proteins. Many components require membrane transport and insertion, complex assembly and cofactor incorporation. All these processes are mediated by fine‐tuned stable and transient protein–protein interactions. Recently, an interactomic approach was used to determine the exact protein–protein interactions involved in the assembly of the denitrification apparatus of Pseudomonas aeruginosa. Both subunits of the NO reductase NorBC, combined with the flavoprotein NosR, serve as a membrane‐localized assembly platform for the attachment of the nitrate reductase NarGHI, the periplasmic nitrite reductase NirS via its maturation factor NirF and the N2O reductase NosZ through NosR. A nitrate transporter (NarK2), the corresponding regulatory system NarXL, various nitrite (NirEJMNQ) and N2O reductase (NosFL) maturation proteins are also part of the complex. Primary dehydrogenases, ATP synthase, most enzymes of the TCA cycle, and the SEC protein export system, as well as a number of other proteins, were found to interact with the denitrification complex. Finally, a protein complex composed of the flagella protein FliC, nitrite reductase NirS and the chaperone DnaK required for flagella formation was found in the periplasm of P. aeruginosa. This work demonstrated that the interactomic approach allows for the identification and characterization of stable and transient protein–protein complexes and interactions involved in the assembly and function of multi‐enzyme complexes.
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Affiliation(s)
| | - Kenneth N Timmis
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, Braunschweig, Germany
| | - Martina Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, Braunschweig, Germany
| | - Dieter Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology BRICS, Technische Universität Braunschweig, Rebenring 56, Braunschweig, Germany
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40
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Ebert M, Schweyen P, Bröring M, Laass S, Härtig E, Jahn D. Heme and nitric oxide binding by the transcriptional regulator DnrF from the marine bacterium Dinoroseobacter shibae increases napD promoter affinity. J Biol Chem 2017; 292:15468-15480. [PMID: 28765283 DOI: 10.1074/jbc.m117.798728] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 05/24/2017] [Revised: 07/24/2017] [Indexed: 12/27/2022] Open
Abstract
Under oxygen-limiting conditions, the marine bacterium Dinoroseobacter shibae DFL12T generates energy via denitrification, a respiratory process in which nitric oxide (NO) is an intermediate. Accumulation of NO may cause cytotoxic effects. The response to this nitrosative (NO-triggered) stress is controlled by the Crp/Fnr-type transcriptional regulator DnrF. We analyzed the response to NO and the mechanism of NO sensing by the DnrF regulator. Using reporter gene fusions and transcriptomics, here we report that DnrF selectively repressed nitrate reductase (nap) genes, preventing further NO formation. In addition, DnrF induced the expression of the NO reductase genes (norCB), which promote NO consumption. We used UV-visible and EPR spectroscopy to characterize heme binding to DnrF and subsequent NO coordination. DnrF detects NO via its bound heme cofactor. We found that the dimeric DnrF bound one molecule of heme per subunit. Purified recombinant apo-DnrF bound its target promoter sequences (napD, nosR2, norC, hemA, and dnrE) in electromobility shift assays, and we identified a specific palindromic DNA-binding site 5'-TTGATN4ATCAA-3' in these target sequences via mutagenesis studies. Most importantly, successive addition of heme as well as heme and NO to purified recombinant apo-DnrF protein increased affinity of the holo-DnrF for its specific binding motif in the napD promoter. On the basis of these results, we propose a model for the DnrF-mediated NO stress response of this marine bacterium.
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Affiliation(s)
- Matthias Ebert
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig
| | - Peter Schweyen
- the Institute for Inorganic and Analytical Chemistry, Technische Universität Braunschweig, Hagenring 30, D-38106 Braunschweig
| | - Martin Bröring
- the Institute for Inorganic and Analytical Chemistry, Technische Universität Braunschweig, Hagenring 30, D-38106 Braunschweig
| | - Sebastian Laass
- the Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, and
| | - Elisabeth Härtig
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig,
| | - Dieter Jahn
- the Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, D-38106 Braunschweig, Germany
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41
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Jahn D, Crosby E. OLDER MALE VETERANS’ RELATIONSHIPS, HELP-SEEKING ATTITUDES, AND SUICIDE RISK FACTORS. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.3560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- D. Jahn
- University of Maryland School of Medicine, Baltimore, Maryland,
- VA Capitol Health Care Network (VISN 5) Mental Illness Research, Education, and Clinical Center (MIRECC), Baltimore, Maryland
| | - E. Crosby
- VA Capitol Health Care Network (VISN 5) Mental Illness Research, Education, and Clinical Center (MIRECC), Baltimore, Maryland
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42
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Jahn D. INTERACTIONS WITH THE HEALTHCARE SYSTEM AND SUICIDE RISK FACTORS AMONG OLDER MALE VETERANS. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.2540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- D. Jahn
- University of Maryland School of Medicine, Baltimore, Maryland,
- VA Capitol Health Care Network (VISN 5) Mental Illness Research, Education, and Clinical Center, Baltimore, Maryland
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43
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Riedel T, Wetzel D, Hofmann JD, Plorin SPEO, Dannheim H, Berges M, Zimmermann O, Bunk B, Schober I, Spröer C, Liesegang H, Jahn D, Overmann J, Groß U, Neumann-Schaal M. High metabolic versatility of different toxigenic and non-toxigenic Clostridioides difficile isolates. Int J Med Microbiol 2017; 307:311-320. [PMID: 28619474 DOI: 10.1016/j.ijmm.2017.05.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/22/2017] [Accepted: 05/28/2017] [Indexed: 12/14/2022] Open
Abstract
Clostridioides difficile (formerly Clostridium difficile) is a major nosocomial pathogen with an increasing number of community-acquired infections causing symptoms from mild diarrhea to life-threatening colitis. The pathogenicity of C. difficile is considered to be mainly associated with the production of genome-encoded toxins A and B. In addition, some strains also encode and express the binary toxin CDT. However; a large number of non-toxigenic C. difficile strains have been isolated from the human gut and the environment. In this study, we characterized the growth behavior, motility and fermentation product formation of 17 different C. difficile isolates comprising five different major genomic clades and five different toxin inventories in relation to the C. difficile model strains 630Δerm and R20291. Within 33 determined fermentation products, we identified two yet undescribed products (5-methylhexanoate and 4-(methylthio)-butanoate) of C. difficile. Our data revealed major differences in the fermentation products obtained after growth in a medium containing casamino acids and glucose as carbon and energy source. While the metabolism of branched chain amino acids remained comparable in all isolates, the aromatic amino acid uptake and metabolism and the central carbon metabolism-associated fermentation pathways varied strongly between the isolates. The patterns obtained followed neither the classification of the clades nor the ribotyping patterns nor the toxin distribution. As the toxin formation is strongly connected to the metabolism, our data allow an improved differentiation of C. difficile strains. The observed metabolic flexibility provides the optimal basis for the adaption in the course of infection and to changing conditions in different environments including the human gut.
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Affiliation(s)
- Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Daniela Wetzel
- University Medical Center Göttingen, Institute of Medical Microbiology, Kreuzbergring 57, 37075 Göttingen, Germany
| | - Julia Danielle Hofmann
- Technische Universität Braunschweig, Department of Bioinformatics and Biochemistry, Rebenring 56, 38106 Braunschweig, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Simon Paul Erich Otto Plorin
- University Medical Center Göttingen, Institute of Medical Microbiology, Kreuzbergring 57, 37075 Göttingen, Germany
| | - Henning Dannheim
- Technische Universität Braunschweig, Department of Bioinformatics and Biochemistry, Rebenring 56, 38106 Braunschweig, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Mareike Berges
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany; Technische Universität Braunschweig, Department of Microbiology, Rebenring 56, 38106 Braunschweig, Germany
| | - Ortrud Zimmermann
- University Medical Center Göttingen, Institute of Medical Microbiology, Kreuzbergring 57, 37075 Göttingen, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Isabel Schober
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Heiko Liesegang
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August-University Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany; Technische Universität Braunschweig, Department of Microbiology, Rebenring 56, 38106 Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Uwe Groß
- University Medical Center Göttingen, Institute of Medical Microbiology, Kreuzbergring 57, 37075 Göttingen, Germany; Göttingen International Health Network, Göttingen, Germany
| | - Meina Neumann-Schaal
- Technische Universität Braunschweig, Department of Bioinformatics and Biochemistry, Rebenring 56, 38106 Braunschweig, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.
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44
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Blaženović I, Kind T, Torbašinović H, Obrenović S, Mehta SS, Tsugawa H, Wermuth T, Schauer N, Jahn M, Biedendieck R, Jahn D, Fiehn O. Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy. J Cheminform 2017; 9:32. [PMID: 29086039 PMCID: PMC5445034 DOI: 10.1186/s13321-017-0219-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/15/2017] [Indexed: 11/10/2022] Open
Abstract
In mass spectrometry-based untargeted metabolomics, rarely more than 30% of the compounds are identified. Without the true identity of these molecules it is impossible to draw conclusions about the biological mechanisms, pathway relationships and provenance of compounds. The only way at present to address this discrepancy is to use in silico fragmentation software to identify unknown compounds by comparing and ranking theoretical MS/MS fragmentations from target structures to experimental tandem mass spectra (MS/MS). We compared the performance of four publicly available in silico fragmentation algorithms (MetFragCL, CFM-ID, MAGMa+ and MS-FINDER) that participated in the 2016 CASMI challenge. We found that optimizing the use of metadata, weighting factors and the manner of combining different tools eventually defined the ultimate outcomes of each method. We comprehensively analysed how outcomes of different tools could be combined and reached a final success rate of 93% for the training data, and 87% for the challenge data, using a combination of MAGMa+, CFM-ID and compound importance information along with MS/MS matching. Matching MS/MS spectra against the MS/MS libraries without using any in silico tool yielded 60% correct hits, showing that the use of in silico methods is still important.
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Affiliation(s)
- Ivana Blaženović
- Technische Universität Braunschweig - Institute of Microbiology, Brunswick, Germany
- Metabolomic Discoveries GmbH, Potsdam, Germany
- NIH West Coast Metabolomics Center, UC Davis Genome Center, Room 1313, 451 Health Sci Drive, Davis, CA 95616 USA
| | - Tobias Kind
- NIH West Coast Metabolomics Center, UC Davis Genome Center, Room 1313, 451 Health Sci Drive, Davis, CA 95616 USA
| | | | | | - Sajjan S. Mehta
- NIH West Coast Metabolomics Center, UC Davis Genome Center, Room 1313, 451 Health Sci Drive, Davis, CA 95616 USA
| | - Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa Japan
| | - Tobias Wermuth
- NIH West Coast Metabolomics Center, UC Davis Genome Center, Room 1313, 451 Health Sci Drive, Davis, CA 95616 USA
| | | | - Martina Jahn
- Technische Universität Braunschweig - Institute of Microbiology, Brunswick, Germany
| | - Rebekka Biedendieck
- Technische Universität Braunschweig - Institute of Microbiology, Brunswick, Germany
| | - Dieter Jahn
- Technische Universität Braunschweig - Institute of Microbiology, Brunswick, Germany
| | - Oliver Fiehn
- NIH West Coast Metabolomics Center, UC Davis Genome Center, Room 1313, 451 Health Sci Drive, Davis, CA 95616 USA
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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45
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Ebert M, Laaß S, Thürmer A, Roselius L, Eckweiler D, Daniel R, Härtig E, Jahn D. FnrL and Three Dnr Regulators Are Used for the Metabolic Adaptation to Low Oxygen Tension in Dinoroseobacter shibae. Front Microbiol 2017; 8:642. [PMID: 28473807 PMCID: PMC5398030 DOI: 10.3389/fmicb.2017.00642] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 01/15/2017] [Accepted: 03/29/2017] [Indexed: 11/14/2022] Open
Abstract
The heterotrophic marine bacterium Dinoroseobacter shibae utilizes aerobic respiration and anaerobic denitrification supplemented with aerobic anoxygenic photosynthesis for energy generation. The aerobic to anaerobic transition is controlled by four Fnr/Crp family regulators in a unique cascade-type regulatory network. FnrL is utilizing an oxygen-sensitive Fe-S cluster for oxygen sensing. Active FnrL is inducing most operons encoding the denitrification machinery and the corresponding heme biosynthesis. Activation of gene expression of the high oxygen affinity cbb3-type and repression of the low affinity aa3-type cytochrome c oxidase is mediated by FnrL. Five regulator genes including dnrE and dnrF are directly controlled by FnrL. Multiple genes of the universal stress protein (USP) and cold shock response are further FnrL targets. DnrD, most likely sensing NO via a heme cofactor, co-induces genes of denitrification, heme biosynthesis, and the regulator genes dnrE and dnrF. DnrE is controlling genes for a putative Na+/H+ antiporter, indicating a potential role of a Na+ gradient under anaerobic conditions. The formation of the electron donating primary dehydrogenases is coordinated by FnrL and DnrE. Many plasmid encoded genes were DnrE regulated. DnrF is controlling directly two regulator genes including the Fe-S cluster biosynthesis regulator iscR, genes of the electron transport chain and the glutathione metabolism. The genes for nitrate reductase and CO dehydrogenase are repressed by DnrD and DnrF. Both regulators in concert with FnrL are inducing the photosynthesis genes. One of the major denitrification operon control regions, the intergenic region between nirS and nosR2, contains one Fnr/Dnr binding site. Using regulator gene mutant strains, lacZ-reporter gene fusions in combination with promoter mutagenesis, the function of the single Fnr/Dnr binding site for FnrL-, DnrD-, and partly DnrF-dependent nirS and nosR2 transcriptional activation was shown. Overall, the unique regulatory network of the marine bacterium D. shibae for the transition from aerobic to anaerobic growth composed of four Crp/Fnr family regulators was elucidated.
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Affiliation(s)
- Matthias Ebert
- Institute of Microbiology, Technische Universität BraunschweigBraunschweig, Germany
| | - Sebastian Laaß
- Institute for Molecular Biosciences, Goethe-University FrankfurtFrankfurt, Germany
| | - Andrea Thürmer
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University GöttingenGöttingen, Germany
| | - Louisa Roselius
- Braunschweig Integrated Centre of Systems Biology, Technische Universität BraunschweigBraunschweig, Germany
| | - Denitsa Eckweiler
- Braunschweig Integrated Centre of Systems Biology, Technische Universität BraunschweigBraunschweig, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University GöttingenGöttingen, Germany
| | - Elisabeth Härtig
- Institute of Microbiology, Technische Universität BraunschweigBraunschweig, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology, Technische Universität BraunschweigBraunschweig, Germany
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Dailey HA, Dailey TA, Gerdes S, Jahn D, Jahn M, O'Brian MR, Warren MJ. Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product. Microbiol Mol Biol Rev 2017; 81:e00048-16. [PMID: 28123057 PMCID: PMC5312243 DOI: 10.1128/mmbr.00048-16] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [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] [Indexed: 02/08/2023] Open
Abstract
The advent of heme during evolution allowed organisms possessing this compound to safely and efficiently carry out a variety of chemical reactions that otherwise were difficult or impossible. While it was long assumed that a single heme biosynthetic pathway existed in nature, over the past decade, it has become clear that there are three distinct pathways among prokaryotes, although all three pathways utilize a common initial core of three enzymes to produce the intermediate uroporphyrinogen III. The most ancient pathway and the only one found in the Archaea converts siroheme to protoheme via an oxygen-independent four-enzyme-step process. Bacteria utilize the initial core pathway but then add one additional common step to produce coproporphyrinogen III. Following this step, Gram-positive organisms oxidize coproporphyrinogen III to coproporphyrin III, insert iron to make coproheme, and finally decarboxylate coproheme to protoheme, whereas Gram-negative bacteria first decarboxylate coproporphyrinogen III to protoporphyrinogen IX and then oxidize this to protoporphyrin IX prior to metal insertion to make protoheme. In order to adapt to oxygen-deficient conditions, two steps in the bacterial pathways have multiple forms to accommodate oxidative reactions in an anaerobic environment. The regulation of these pathways reflects the diversity of bacterial metabolism. This diversity, along with the late recognition that three pathways exist, has significantly slowed advances in this field such that no single organism's heme synthesis pathway regulation is currently completely characterized.
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Affiliation(s)
- Harry A Dailey
- Department of Microbiology, Department of Biochemistry and Molecular Biology, and Biomedical and Health Sciences Institute, University of Georgia, Athens, Georgia, USA
| | - Tamara A Dailey
- Department of Microbiology, Department of Biochemistry and Molecular Biology, and Biomedical and Health Sciences Institute, University of Georgia, Athens, Georgia, USA
| | - Svetlana Gerdes
- Fellowship for Interpretation of Genomes, Burr Ridge, Illinois, USA
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universitaet Braunschweig, Braunschweig, Germany
| | - Martina Jahn
- Institute of Microbiology, Technische Universitaet Braunschweig, Braunschweig, Germany
| | - Mark R O'Brian
- Department of Biochemistry, University at Buffalo, The State University of New York, Buffalo, New York, USA
| | - Martin J Warren
- Department of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
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Nuss AM, Schuster F, Roselius L, Klein J, Bücker R, Herbst K, Heroven AK, Pisano F, Wittmann C, Münch R, Müller J, Jahn D, Dersch P. A Precise Temperature-Responsive Bistable Switch Controlling Yersinia Virulence. PLoS Pathog 2016; 12:e1006091. [PMID: 28006011 PMCID: PMC5179001 DOI: 10.1371/journal.ppat.1006091] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/27/2016] [Indexed: 11/19/2022] Open
Abstract
Different biomolecules have been identified in bacterial pathogens that sense changes in temperature and trigger expression of virulence programs upon host entry. However, the dynamics and quantitative outcome of this response in individual cells of a population, and how this influences pathogenicity are unknown. Here, we address these questions using a thermosensing virulence regulator of an intestinal pathogen (RovA of Yersinia pseudotuberculosis) as a model. We reveal that this regulator is part of a novel thermoresponsive bistable switch, which leads to high- and low-invasive subpopulations within a narrow temperature range. The temperature range in which bistability is observed is defined by the degradation and synthesis rate of the regulator, and is further adjustable via a nutrient-responsive regulator. The thermoresponsive switch is also characterized by a hysteretic behavior in which activation and deactivation occurred on vastly different time scales. Mathematical modeling accurately mirrored the experimental behavior and predicted that the thermoresponsiveness of this sophisticated bistable switch is mainly determined by the thermo-triggered increase of RovA proteolysis. We further observed RovA ON and OFF subpopulations of Y. pseudotuberculosis in the Peyer’s patches and caecum of infected mice, and that changes in the RovA ON/OFF cell ratio reduce tissue colonization and overall virulence. This points to a bet-hedging strategy in which the thermoresponsive bistable switch plays a key role in adapting the bacteria to the fluctuating conditions encountered as they pass through the host’s intestinal epithelium and suggests novel strategies for the development of antimicrobial therapies. The ability of pathogens to sense temperature changes when they enter their mammalian hosts from the environment is crucial to optimize their fitness and adjust expression of their virulence programs. Until now it has been assumed that all cells within a population participate in the thermo-triggered adaptive response. Here, we show that a small subpopulation of an enteric pathogen does not follow thermo-induced reprogramming when the bacteria pass the intestinal epithelial layer. Observed heterogeneity is promoted by a new type of bistable switch, implicating a highly precise, thermoresponsive control element. Moreover, we demonstrate that this regulatory implement is important for virulence as it prepares the pathogen for sudden, unpredictable fluctuations encountered during host entry and exit.
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Affiliation(s)
- Aaron Mischa Nuss
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Franziska Schuster
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Louisa Roselius
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | - Johannes Klein
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | - René Bücker
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Katharina Herbst
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ann Kathrin Heroven
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Fabio Pisano
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Richard Münch
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | - Johannes Müller
- Institute of Mathematics, Technical University Munich, Munich, Germany
- Institute of Computational Biology, Helmholtz Centre Munich, Neuherberg, Germany
| | - Dieter Jahn
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | - Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- * E-mail:
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48
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Weidenbach M, Jahn D, Rehn A, Busch SF, Beltrán-Mejía F, Balzer JC, Koch M. 3D printed dielectric rectangular waveguides, splitters and couplers for 120 GHz. Opt Express 2016; 24:28968-28976. [PMID: 27958561 DOI: 10.1364/oe.24.028968] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We use a 3D printer to fabricate rectangular dielectric single mode waveguides for 120 GHz. The rectangular waveguides consisting of polystyrene showed an attenuation of 6.3 dB/m, which is low enough for short devices. We also characterize 3D printed Y-splitters and a 1x3-splitter based on multimode interference. Further, we construct and measure a variable planar waveguide coupler which can be used as a 3-dB coupler, a cross-coupler and no coupler at all.
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49
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Füller JJ, Röpke R, Krausze J, Rennhack KE, Daniel NP, Blankenfeldt W, Schulz S, Jahn D, Moser J. Biosynthesis of Violacein, Structure and Function of l-Tryptophan Oxidase VioA from Chromobacterium violaceum. J Biol Chem 2016; 291:20068-84. [PMID: 27466367 DOI: 10.1074/jbc.m116.741561] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Indexed: 11/06/2022] Open
Abstract
Violacein is a natural purple pigment of Chromobacterium violaceum with potential medical applications as antimicrobial, antiviral, and anticancer drugs. The initial step of violacein biosynthesis is the oxidative conversion of l-tryptophan into the corresponding α-imine catalyzed by the flavoenzyme l-tryptophan oxidase (VioA). A substrate-related (3-(1H-indol-3-yl)-2-methylpropanoic acid) and a product-related (2-(1H-indol-3-ylmethyl)prop-2-enoic acid) competitive VioA inhibitor was synthesized for subsequent kinetic and x-ray crystallographic investigations. Structures of the binary VioA·FADH2 and of the ternary VioA·FADH2·2-(1H-indol-3-ylmethyl)prop-2-enoic acid complex were resolved. VioA forms a "loosely associated" homodimer as indicated by small-angle x-ray scattering experiments. VioA belongs to the glutathione reductase family 2 of FAD-dependent oxidoreductases according to the structurally conserved cofactor binding domain. The substrate-binding domain of VioA is mainly responsible for the specific recognition of l-tryptophan. Other canonical amino acids were efficiently discriminated with a minor conversion of l-phenylalanine. Furthermore, 7-aza-tryptophan, 1-methyl-tryptophan, 5-methyl-tryptophan, and 5-fluoro-tryptophan were efficient substrates of VioA. The ternary product-related VioA structure indicated involvement of protein domain movement during enzyme catalysis. Extensive structure-based mutagenesis in combination with enzyme kinetics (using l-tryptophan and substrate analogs) identified Arg(64), Lys(269), and Tyr(309) as key catalytic residues of VioA. An increased enzyme activity of protein variant H163A in the presence of l-phenylalanine indicated a functional role of His(163) in substrate binding. The combined structural and mutational analyses lead to the detailed understanding of VioA substrate recognition. Related strategies for the in vivo synthesis of novel violacein derivatives are discussed.
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Affiliation(s)
| | - René Röpke
- the Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, D-38106 Braunschweig, and
| | - Joern Krausze
- the Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | | | | | - Wulf Blankenfeldt
- the Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig
| | - Stefan Schulz
- the Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, D-38106 Braunschweig, and
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50
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Patzelt D, Michael V, Päuker O, Ebert M, Tielen P, Jahn D, Tomasch J, Petersen J, Wagner-Döbler I. Gene Flow Across Genus Barriers - Conjugation of Dinoroseobacter shibae's 191-kb Killer Plasmid into Phaeobacter inhibens and AHL-mediated Expression of Type IV Secretion Systems. Front Microbiol 2016; 7:742. [PMID: 27303368 PMCID: PMC4886583 DOI: 10.3389/fmicb.2016.00742] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 01/23/2016] [Accepted: 05/03/2016] [Indexed: 01/24/2023] Open
Abstract
Rhodobacteraceae harbor a conspicuous wealth of extrachromosomal replicons (ECRs) and therefore the exchange of genetic material via horizontal transfer has been supposed to be a major evolutionary driving force. Many plasmids in this group encode type IV secretion systems (T4SS) that are expected to mediate transfer of proteins and/or DNA into host cells, but no experimental evidence of either has yet been provided. Dinoroseobacter shibae, a species of the Roseobacter group within the Rhodobacteraceae family, contains five ECRs that are crucial for anaerobic growth, survival under starvation and the pathogenicity of this model organism. Here we tagged two syntenous but compatible RepABC-type plasmids of 191 and 126-kb size, each encoding a T4SS, with antibiotic resistance genes and demonstrated their conjugational transfer into a distantly related Roseobacter species, namely Phaeobacter inhibens. Pulsed field gel electrophoresis showed transfer of those replicons into the recipient both individually but also together documenting the efficiency of conjugation. We then studied the influence of externally added quorum sensing (QS) signals on the expression of the T4SS located on the sister plasmids. A QS deficient D. shibae null mutant (ΔluxI1) lacking synthesis of N-acyl-homoserine lactones (AHLs) was cultivated with a wide spectrum of chemically diverse long-chain AHLs. All AHLs with lengths of the acid side-chain ≥14 reverted the ΔluxI1 phenotype to wild-type. Expression of the T4SS was induced up to log2 ∼3fold above wild-type level. We hypothesize that conjugation in roseobacters is QS-controlled and that the QS system may detect a wide array of long-chain AHLs at the cell surface.
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Affiliation(s)
- Diana Patzelt
- Department of Microbiology, Microbial Communication, Helmholtz-Centre for Infection Research Braunschweig, Germany
| | - Victoria Michael
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Orsola Päuker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Matthias Ebert
- Braunschweig University of Technology Braunschweig, Germany
| | - Petra Tielen
- Braunschweig University of Technology Braunschweig, Germany
| | - Dieter Jahn
- Braunschweig University of Technology Braunschweig, Germany
| | - Jürgen Tomasch
- Department of Microbiology, Microbial Communication, Helmholtz-Centre for Infection Research Braunschweig, Germany
| | - Jörn Petersen
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Irene Wagner-Döbler
- Department of Microbiology, Microbial Communication, Helmholtz-Centre for Infection Research Braunschweig, Germany
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