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Koblitz J. Metabolism from the magic angle. Nat Chem Biol 2023; 19:538-539. [PMID: 37117920 DOI: 10.1038/s41589-023-01317-2] [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: 04/30/2023]
Affiliation(s)
- Julia Koblitz
- Department of Bioinformatics and Databases, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
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Koblitz J, Halama P, Spring S, Thiel V, Baschien C, Hahnke R, Pester M, Overmann J, Reimer L. MediaDive: the expert-curated cultivation media database. Nucleic Acids Res 2022; 51:D1531-D1538. [PMID: 36134710 PMCID: PMC9825534 DOI: 10.1093/nar/gkac803] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/29/2022] [Accepted: 09/09/2022] [Indexed: 01/30/2023] Open
Abstract
We present MediaDive (https://mediadive.dsmz.de), a comprehensive and expert-curated cultivation media database, which comprises recipes, instructions and molecular compositions of >3200 standardized cultivation media for >40 000 microbial strains from all domains of life. MediaDive is designed to enable broad range applications from every-day-use in research and diagnostic laboratories to knowledge-driven support of new media design and artificial intelligence-driven data mining. It offers a number of intuitive search functions and comparison tools, for example to identify media for related taxonomic groups and to integrate strain-specific modifications. Besides classical PDF archiving and printing, the state-of-the-art website allows paperless use of media recipes on mobile devices for convenient wet-lab use. In addition, data can be retrieved using a RESTful web service for large-scale data analyses. An internal editor interface ensures continuous extension and curation of media by cultivation experts from the Leibniz Institute DSMZ, which is interlinked with the growing microbial collections at DSMZ. External user engagement is covered by a dedicated media builder tool. The standardized and programmatically accessible data will foster new approaches for the design of cultivation media to target the vast majority of uncultured microorganisms.
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Affiliation(s)
- Julia Koblitz
- To whom correspondence should be addressed. Tel: +49 531 2616 313; Fax: +49 531 2616 418;
| | - Philipp Halama
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Stefan Spring
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Vera Thiel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Christiane Baschien
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Richard L Hahnke
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael Pester
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany,Technical University of Braunschweig, Institute for Microbiology, Braunschweig, Germany
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Abstract
Human and animal cell lines serve as model systems in a wide range of life sciences such as cancer and infection research or drug screening. Reproducible data are highly dependent on authenticated, contaminant-free cell lines, no better delivered than by the official and certified biorepositories. Offering a web portal to high-throughput information on these model systems will facilitate working with and comparing to these references by data otherwise dispersed at different sources. We here provide DSMZCellDive to access a comprehensive data source on human and animal cell lines, freely available at celldive.dsmz.de. A wide variety of data sources are generated such as RNA-seq transcriptome data and STR (short tandem repeats) profiles. Several starting points ease entering the database via browsing, searching or visualising. This web tool is designed for further expansion on meta and high-throughput data to be generated in future. Explicated examples for the power of this novel tool include analysis of B-cell differentiation markers, homeo-oncogene expression, and measurement of genomic loss of heterozygosities by an enlarged STR panel of 17 loci. Sharing the data on cell lines by the biorepository itself will be of benefit to the scientific community since it (1) supports the selection of appropriate model cell lines, (2) ensures reliability, (3) avoids misleading data, (4) saves on additional experimentals, and (5) serves as reference for genomic and gene expression data.
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Affiliation(s)
- Julia Koblitz
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
| | - Wilhelm G. Dirks
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
| | - Sonja Eberth
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
| | - Stefan Nagel
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
| | - Laura Steenpass
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
| | - Claudia Pommerenke
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
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Reimer LC, Sardà Carbasse J, Koblitz J, Ebeling C, Podstawka A, Overmann J. BacDive in 2022: the knowledge base for standardized bacterial and archaeal data. Nucleic Acids Res 2022; 50:D741-D746. [PMID: 34718743 PMCID: PMC8728306 DOI: 10.1093/nar/gkab961] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [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: 09/07/2021] [Revised: 09/30/2021] [Accepted: 10/05/2021] [Indexed: 11/24/2022] Open
Abstract
The bacterial metadatabase BacDive (https://bacdive.dsmz.de) has developed into a leading database for standardized prokaryotic data on strain level. With its current release (07/2021) the database offers information for 82 892 bacterial and archaeal strains covering taxonomy, morphology, cultivation, metabolism, origin, and sequence information within 1048 data fields. By integrating high-quality data from additional culture collections as well as detailed information from species descriptions, the amount of data provided has increased by 30% over the past three years. A newly developed query builder tool in the advanced search now allows complex database queries. Thereby bacterial strains can be systematically searched based on combinations of their attributes, e.g. growth and metabolic features for biotechnological applications or to identify gaps in the present knowledge about bacteria. A new interactive dashboard provides a statistic overview over the most important data fields. Additional new features are improved genomic sequence data, integrated NCBI TaxIDs and links to BacMedia, the new sister database on cultivation media. To improve the findability and interpretation of data through search engines, data in BacDive are annotated with bioschemas.org terms.
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Affiliation(s)
- Lorenz Christian Reimer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Joaquim Sardà Carbasse
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Julia Koblitz
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Christian Ebeling
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Adam Podstawka
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Wolf J, Koblitz J, Albersmeier A, Kalinowski J, Siebers B, Schomburg D, Neumann-Schaal M. Utilization of Phenol as Carbon Source by the Thermoacidophilic Archaeon Saccharolobus solfataricus P2 Is Limited by Oxygen Supply and the Cellular Stress Response. Front Microbiol 2021; 11:587032. [PMID: 33488537 PMCID: PMC7820114 DOI: 10.3389/fmicb.2020.587032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/08/2020] [Indexed: 12/20/2022] Open
Abstract
Present in many industrial effluents and as common degradation product of organic matter, phenol is a widespread compound which may cause serious environmental problems, due to its toxicity to animals and humans. Degradation of phenol from the environment by mesophilic bacteria has been studied extensively over the past decades, but only little is known about phenol biodegradation at high temperatures or low pH. In this work we studied phenol degradation in the thermoacidophilic archaeon Saccharolobus solfataricus P2 (basonym: Sulfolobus solfataricus) under extreme conditions (80°C, pH 3.5). We combined metabolomics and transcriptomics together with metabolic modeling to elucidate the organism’s response to growth with phenol as sole carbon source. Although S. solfataricus is able to utilize phenol for biomass production, the carbon source induces profound stress reactions, including genome rearrangement as well as a strong intracellular accumulation of polyamines. Furthermore, computational modeling revealed a 40% higher oxygen demand for substrate oxidation, compared to growth on glucose. However, only 16.5% of oxygen is used for oxidation of phenol to catechol, resulting in a less efficient integration of carbon into the biomass. Finally, our data underlines the importance of the phenol meta-degradation pathway in S. solfataricus and enables us to predict enzyme candidates involved in the degradation processes downstream of 2-hydroxymucconic acid.
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Affiliation(s)
- Jacqueline Wolf
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Julia Koblitz
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | | | - Jörn Kalinowski
- Center for Biotechnology-CeBiTec, Universität Bielefeld, Bielefeld, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Meina Neumann-Schaal
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Junior Research Group Bacterial Metabolomics, Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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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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Abstract
Metabolic pathways are an important part of systems biology research since they illustrate complex interactions between metabolites, enzymes, and regulators. Pathway maps are drawn to elucidate metabolism or to set data in a metabolic context. We present MetaboMAPS, a web-based platform to visualize numerical data on individual metabolic pathway maps. Metabolic maps can be stored, distributed and downloaded in SVG-format. MetaboMAPS was designed for users without computational background and supports pathway sharing without strict conventions. In addition to existing applications that established standards for well-studied pathways, MetaboMAPS offers a niche for individual, customized pathways beyond common knowledge, supporting ongoing research by creating publication-ready visualizations of experimental data.
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Affiliation(s)
- Julia Koblitz
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
- Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
- Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Meina Neumann-Schaal
- Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, 38106, Germany
- Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
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Abstract
Metabolic pathways are an important part of systems biology research since they illustrate complex interactions between metabolites, enzymes, and regulators. Pathway maps are drawn to elucidate metabolism or to set data in a metabolic context. We present MetaboMAPS, a web-based platform to visualize numerical data on individual metabolic pathway maps. Metabolic maps can be stored, distributed and downloaded in SVG-format. MetaboMAPS was designed for users without computational background and supports pathway sharing without strict conventions. In addition to existing applications that established standards for well-studied pathways, MetaboMAPS offers a niche for individual, customized pathways beyond common knowledge, supporting ongoing research by creating publication-ready visualizations of experimental data.
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Affiliation(s)
- Julia Koblitz
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
- Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
- Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Meina Neumann-Schaal
- Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, 38106, Germany
- Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
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