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1.
mSystems ; 7(6): e0068522, 2022 12 20.
Article de Anglais | MEDLINE | ID: mdl-36445109

RÉSUMÉ

Members of the genus Aromatoleum thrive in diverse habitats and use a broad range of recalcitrant organic molecules coupled to denitrification or O2 respiration. To gain a holistic understanding of the model organism A. aromaticum EbN1T, we studied its catabolic network dynamics in response to 3-(4-hydroxyphenyl)propanoate, phenylalanine, 3-hydroxybenzoate, benzoate, and acetate utilized under nitrate-reducing versus oxic conditions. Integrated multi-omics (transcriptome, proteome, and metabolome) covered most of the catabolic network (199 genes) and allowed for the refining of knowledge of the degradation modules studied. Their substrate-dependent regulation showed differing degrees of specificity, ranging from high with 3-(4-hydroxyphenyl)propanoate to mostly relaxed with benzoate. For benzoate, the transcript and protein formation were essentially constitutive, contrasted by that of anoxia-specific versus oxia-specific metabolite profiles. The matrix factorization of transcriptomic data revealed that the anaerobic modules accounted for most of the variance across the degradation network. The respiration network appeared to be constitutive, both on the transcript and protein levels, except for nitrate reductase (with narGHI expression occurring only under nitrate-reducing conditions). The anoxia/nitrate-dependent transcription of denitrification genes is apparently controlled by three FNR-type regulators as well as by NarXL (all constitutively formed). The resequencing and functional reannotation of the genome fostered a genome-scale metabolic model, which is comprised of 655 enzyme-catalyzed reactions and 731 distinct metabolites. The model predictions for growth rates and biomass yields agreed well with experimental stoichiometric data, except for 3-(4-hydroxyphenyl)propanoate, with which 4-hydroxybenzoate was exported. Taken together, the combination of multi-omics, growth physiology, and a metabolic model advanced our knowledge of an environmentally relevant microorganism that differs significantly from other bacterial model strains. IMPORTANCE Aromatic compounds are abundant constituents not only of natural organic matter but also of bulk industrial chemicals and fuel components of environmental concern. Considering the widespread occurrence of redox gradients in the biosphere, facultative anaerobic degradation specialists can be assumed to play a prominent role in the natural mineralization of organic matter and in bioremediation at contaminated sites. Surprisingly, differential multi-omics profiling of the A. aromaticum EbN1T studied here revealed relaxed regulatory stringency across its four main physiological modi operandi (i.e., O2-independent and O2-dependent degradation reactions versus denitrification and O2 respiration). Combining multi-omics analyses with a genome-scale metabolic model aligned with measured growth performances establishes A. aromaticum EbN1T as a systems-biology model organism and provides unprecedented insights into how this bacterium functions on a holistic level. Moreover, this experimental platform invites future studies on eco-systems and synthetic biology of the environmentally relevant betaproteobacterial Aromatoleum/Azoarcus/Thauera cluster.


Sujet(s)
Propionates , Biologie des systèmes , Anaérobiose , Nitrates , Benzoates
2.
Nucleic Acids Res ; 49(D1): D498-D508, 2021 01 08.
Article de Anglais | MEDLINE | ID: mdl-33211880

RÉSUMÉ

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.


Sujet(s)
Bases de données de protéines , Enzymes/composition chimique , Acétyl coenzyme A/biosynthèse , Arabidopsis/enzymologie , Bacillus subtilis/enzymologie , Imagerie tridimensionnelle , Voies et réseaux métaboliques , Annotation de séquence moléculaire , Moteur de recherche
3.
Nucleic Acids Res ; 47(D1): D542-D549, 2019 01 08.
Article de Anglais | MEDLINE | ID: mdl-30395242

RÉSUMÉ

The BRENDA enzyme database (www.brenda-enzymes.org), recently appointed ELIXIR Core Data Resource, is the main enzyme and enzyme-ligand information system. The core database provides a comprehensive overview on enzymes. A collection of 4.3 million data for ∼84 000 enzymes manually evaluated and extracted from ∼140 000 primary literature references is combined with information obtained by text and data mining, data integration and prediction algorithms. Supplements comprise disease-related data, protein sequences, 3D structures, predicted enzyme locations and genome annotations. Major developments are a revised ligand summary page and the structure search now including a similarity and isomer search. BKMS-react, an integrated database containing known enzyme-catalyzed reactions, is supplemented with further reactions and improved access to pathway connections. In addition to existing enzyme word maps with graphical information of enzyme specific terms, plant word maps have been developed. They show a graphical overview of terms, e.g. enzyme or plant pathogen information, connected to specific plants. An organism summary page showing all relevant information, e.g. taxonomy and synonyms linked to enzyme data, was implemented. Based on a decision by the IUBMB enzyme task force the enzyme class EC 7 has been established for 'translocases', enzymes that catalyze a transport of ions or metabolites across cellular membranes.


Sujet(s)
Bases de données de protéines , Enzymes/composition chimique , Séquence d'acides aminés , Maladie , Enzymes/analyse , Enzymes/génétique , Enzymes/métabolisme , Humains , Ligands , Conformation des protéines
4.
Nucleic Acids Res ; 45(D1): D380-D388, 2017 01 04.
Article de Anglais | MEDLINE | ID: mdl-27924025

RÉSUMÉ

The BRENDA enzyme database (www.brenda-enzymes.org) has developed into the main enzyme and enzyme-ligand information system in its 30 years of existence. The information is manually extracted from primary literature and extended by text mining procedures, integration of external data and prediction algorithms. Approximately 3 million data from 83 000 enzymes and 137 000 literature references constitute the manually annotated core. Text mining procedures extend these data with information on occurrence, enzyme-disease relationships and kinetic data. Prediction algorithms contribute locations and genome annotations. External data and links complete the data with sequences and 3D structures. A total of 206 000 enzyme ligands provide functional and structural data. BRENDA offers a complex query tool engine allowing the users an efficient access to the data via different search methods and explorers. The new design of the BRENDA entry page and the enzyme summary pages improves the user access and the performance. New interactive and intuitive BRENDA pathway maps give an overview on biochemical processes and facilitate the visualization of enzyme, ligand and organism information in the biochemical context. SCOPe and CATH, databases for protein structure classification, are included. New online and video tutorials provide online training for the users. BRENDA is freely available for academic users.


Sujet(s)
Biologie informatique/méthodes , Bases de données de protéines , Enzymes , Algorithmes , Fouille de données , Découverte de médicament , Humains , Ligands , Liaison aux protéines , Logiciel , Navigateur
5.
Nucleic Acids Res ; 43(Database issue): D439-46, 2015 Jan.
Article de Anglais | MEDLINE | ID: mdl-25378310

RÉSUMÉ

The BRENDA enzyme information system (http://www.brenda-enzymes.org/) has developed into an elaborate system of enzyme and enzyme-ligand information obtained from different sources, combined with flexible query systems and evaluation tools. The information is obtained by manual extraction from primary literature, text and data mining, data integration, and prediction algorithms. Approximately 300 million data include enzyme function and molecular data from more than 30,000 organisms. The manually derived core contains 3 million data from 77,000 enzymes annotated from 135,000 literature references. Each entry is connected to the literature reference and the source organism. They are complemented by information on occurrence, enzyme/disease relationships from text mining, sequences and 3D structures from other databases, and predicted enzyme location and genome annotation. Functional and structural data of more than 190,000 enzyme ligands are stored in BRENDA. New features improving the functionality and analysis tools were implemented. The human anatomy atlas CAVEman is linked to the BRENDA Tissue Ontology terms providing a connection between anatomical and functional enzyme data. Word Maps for enzymes obtained from PubMed abstracts highlight application and scientific relevance of enzymes. The EnzymeDetector genome annotation tool and the reaction database BKM-react including reactions from BRENDA, KEGG and MetaCyc were improved. The website was redesigned providing new query options.


Sujet(s)
Bases de données de protéines , Enzymes/composition chimique , Enzymes/métabolisme , Enzymes/génétique , Humains , Internet , Ligands
6.
Nucleic Acids Res ; 41(Database issue): D764-72, 2013 Jan.
Article de Anglais | MEDLINE | ID: mdl-23203881

RÉSUMÉ

The BRENDA (BRaunschweig ENzyme DAtabase) enzyme portal (http://www.brenda-enzymes.org) is the main information system of functional biochemical and molecular enzyme data and provides access to seven interconnected databases. BRENDA contains 2.7 million manually annotated data on enzyme occurrence, function, kinetics and molecular properties. Each entry is connected to a reference and the source organism. Enzyme ligands are stored with their structures and can be accessed via their names, synonyms or via a structure search. FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) are based on text mining methods and represent a complete survey of PubMed abstracts with information on enzymes in different organisms, tissues or organelles. The supplemental database DRENDA provides more than 910 000 new EC number-disease relations in more than 510 000 references from automatic search and a classification of enzyme-disease-related information. KENDA (Kinetic ENzyme DAta), a new amendment extracts and displays kinetic values from PubMed abstracts. The integration of the EnzymeDetector offers an automatic comparison, evaluation and prediction of enzyme function annotations for prokaryotic genomes. The biochemical reaction database BKM-react contains non-redundant enzyme-catalysed and spontaneous reactions and was developed to facilitate and accelerate the construction of biochemical models.


Sujet(s)
Bases de données de protéines , Enzymes/composition chimique , Enzymes/métabolisme , Maladie , Enzymes/classification , Enzymes/génétique , Internet , Cinétique , Ligands
7.
Nucleic Acids Res ; 39(Database issue): D507-13, 2011 Jan.
Article de Anglais | MEDLINE | ID: mdl-21030441

RÉSUMÉ

BTO, the BRENDA Tissue Ontology (http://www.BTO.brenda-enzymes.org) represents a comprehensive structured encyclopedia of tissue terms. The project started in 2003 to create a connection between the enzyme data collection of the BRENDA enzyme database and a structured network of source tissues and cell types. Currently, BTO contains more than 4600 different anatomical structures, tissues, cell types and cell lines, classified under generic categories corresponding to the rules and formats of the Gene Ontology Consortium and organized as a directed acyclic graph (DAG). Most of the terms are endowed with comments on their derivation or definitions. The content of the ontology is constantly curated with ∼1000 new terms each year. Four different types of relationships between the terms are implemented. A versatile web interface with several search and navigation functionalities allows convenient online access to the BTO and to the enzymes isolated from the tissues. Important areas of applications of the BTO terms are the detection of enzymes in tissues and the provision of a solid basis for text-mining approaches in this field. It is widely used by lab scientists, curators of genomic and biochemical databases and bioinformaticians. The BTO is freely available at http://www.obofoundry.org.


Sujet(s)
Bases de données factuelles , Enzymes , Vocabulaire contrôlé , Lignée cellulaire , Cellules/classification , Cellules/enzymologie , Dictionnaires comme sujet , Intégration de systèmes , Interface utilisateur
8.
Nucleic Acids Res ; 39(Database issue): D670-6, 2011 Jan.
Article de Anglais | MEDLINE | ID: mdl-21062828

RÉSUMÉ

The BRENDA (BRaunschweig ENzyme Database, http://www.brenda-enzymes.org) enzyme information system is the main collection of enzyme functional and property data for the scientific community. The majority of the data are manually extracted from the primary literature. The content covers information on function, structure, occurrence, preparation and application of enzymes as well as properties of mutants and engineered variants. The number of manually annotated references increased by 30% to more than 100,000, the number of ligand structures by 45% to almost 100,000. New query, analysis and data management tools were implemented to improve data processing, data presentation, data input and data access. BRENDA now provides new viewing options such as the display of the statistics of functional parameters and the 3D view of protein sequence and structure features. Furthermore a ligand summary shows comprehensive information on the BRENDA ligands. The enzymes are linked to their respective pathways and can be viewed in pathway maps. The disease text mining part is strongly enhanced. It is possible to submit new, not yet classified enzymes to BRENDA, which then are reviewed and classified by the International Union of Biochemistry and Molecular Biology. A new SBML output format of BRENDA kinetic data allows the construction of organism-specific metabolic models.


Sujet(s)
Bases de données de protéines , Enzymes/composition chimique , Enzymes/génétique , Enzymes/métabolisme , Ligands , Voies et réseaux métaboliques , Conformation des protéines , Logiciel
9.
Methods Mol Biol ; 609: 113-28, 2010.
Article de Anglais | MEDLINE | ID: mdl-20221916

RÉSUMÉ

Enzymes are catalysts for the chemical reactions in the metabolism of all organisms and play a key role in the regulation of metabolic steps within the cells, as drug targets, and in a wide range of biotechnological applications. With respect to reaction type, they are grouped into six classes, namely oxidoreductases, transferases, hydrolases, lyases, and ligases. EC-Numbers are assigned by the IUBMB. Enzyme functional databases cover a wide range of properties and functions, such as occurrence, kinetics of enzyme-catalyzed reactions, structure, or metabolic function. BRENDA stores a large variety of different data for all classified enzymes whereas KEGG, MEROPS, MetaCyc, REBASE, CAzy, ESTHER, PeroxiBase, and KinBase specialize in either certain aspects of enzyme function or specific enzyme classes, organisms, or metabolic pathways. Databases covering enzyme nomenclature are ExplorEnz, SIB-ENZYME, and IntEnz.


Sujet(s)
Fouille de données , Bases de données de protéines , Enzymes/classification , Biologie des systèmes , Terminologie comme sujet , Animaux , Catalyse , Infographie , Enzymes/composition chimique , Enzymes/génétique , Enzymes/métabolisme , Humains , Internet , Cinétique , Conformation des protéines , Logiciel , Relation structure-activité , Intégration de systèmes , Interface utilisateur
10.
PLoS Comput Biol ; 6(1): e1000661, 2010 Jan 29.
Article de Anglais | MEDLINE | ID: mdl-20126531

RÉSUMÉ

A wide range of research areas in molecular biology and medical biochemistry require a reliable enzyme classification system, e.g., drug design, metabolic network reconstruction and system biology. When research scientists in the above mentioned areas wish to unambiguously refer to an enzyme and its function, the EC number introduced by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) is used. However, each and every one of these applications is critically dependent upon the consistency and reliability of the underlying data for success. We have developed tools for the validation of the EC number classification scheme. In this paper, we present validated data of 3788 enzymatic reactions including 229 sub-subclasses of the EC classification system. Over 80% agreement was found between our assignment and the EC classification. For 61 (i.e., only 2.5%) reactions we found that their assignment was inconsistent with the rules of the nomenclature committee; they have to be transferred to other sub-subclasses. We demonstrate that our validation results can be used to initiate corrections and improvements to the EC number classification scheme.


Sujet(s)
Biologie informatique/méthodes , Enzymes , Bases de données de protéines , Enzymes/composition chimique , Enzymes/classification , Reproductibilité des résultats
11.
Bioinformatics ; 25(23): 3135-42, 2009 Dec 01.
Article de Anglais | MEDLINE | ID: mdl-19783831

RÉSUMÉ

BACKGROUND: Enzymes are classified in a numerical classification scheme introduced by the Nomenclature Committee of the IUBMB based on the overall reaction chemistry. Due to the manifold of enzymatic reactions the system has become highly complex. Assignment of enzymes to the enzyme classes requires a detailed knowledge of the system and manual analysis. Frequently rearrangements and deletions of enzymes and sub-subclasses are necessary. RESULTS: We use the Dugundji-Ugi model for coding of biochemical reactions which is based on electron shift patterns occurring during reactions. Changes of the bonds or of non-bonded valence electrons are expressed by reaction matrices. Our program calculates reaction matrices automatically on the sole basis of substrate and product chemical structures based on a new strategy for maximal common substructure determination, which allows an accurate atom mapping of the substrate and product atoms. The system has been tested for a large set of enzymatic reactions including all sub-subclasses of the EC classification system. Altogether 147 different representative reaction operators were found in the classified enzymes, 121 of which are unique with respect to an EC sub-subclass. The other 26 comprise groups of enzymes with very similar reactions, being identical with respect to the bonds formed and broken. CONCLUSION: The analysis and comparison of enzymatic reactions according to their electron shift patterns is defining enzyme groups characterised by unique reaction cores. Our results demonstrate the applicability of the Dugundji-Ugi model as a reasonable pre-classification system allowing an objective and rational view on biochemical reactions. AVAILABILITY: The program to generate reaction matrix descriptors is available upon request.


Sujet(s)
Biologie informatique/méthodes , Enzymes/classification , Biocatalyse , Bases de données de protéines , Enzymes/composition chimique , Enzymes/métabolisme , Cinétique , Modèles théoriques , Spécificité du substrat
12.
Nucleic Acids Res ; 37(Database issue): D588-92, 2009 Jan.
Article de Anglais | MEDLINE | ID: mdl-18984617

RÉSUMÉ

The BRENDA (BRaunschweig ENzyme DAtabase) (http://www.brenda-enzymes.org) represents the largest freely available information system containing a huge amount of biochemical and molecular information on all classified enzymes as well as software tools for querying the database and calculating molecular properties. The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. The data in BRENDA are manually curated from more than 79,000 primary literature references. Each entry is clearly linked to a literature reference, the origin organism and, where available, to the protein sequence of the enzyme protein. A new search option provides the access to protein-specific data. FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) are additional databases created by continuously improved text-mining procedures. These databases ought to provide a complete survey on enzyme data of the literature collection of PubMed. The web service via a SOAP (Simple Object Access Protocol) interface for access to the BRENDA data has been further enhanced.


Sujet(s)
Bases de données de protéines , Enzymes/composition chimique , Enzymes/physiologie , Enzymes/classification , Internet , PubMed , Logiciel
13.
Nucleic Acids Res ; 35(Database issue): D511-4, 2007 Jan.
Article de Anglais | MEDLINE | ID: mdl-17202167

RÉSUMÉ

The BRENDA (BRaunschweig ENzyme DAtabase) enzyme information system (http://www.brenda.uni-koeln.de) is the largest publicly available enzyme information system worldwide. The major parts of its contents are manually extracted from primary literature. It is not restricted to specific groups of enzymes, but includes information on all identified enzymes irrespective of the enzyme's source. The range of data encompasses functional, structural, sequence, localisation, disease-related, isolation, stability information on enzyme and ligand-related data. Each single entry is linked to the enzyme source and to a literature reference. Recently the data repository was complemented by text-mining data in AMENDA (Automatic Mining of ENzyme DAta) and FRENDA (Full Reference ENzyme DAta). A genome browser, membrane protein prediction and full-text search capacities were added. The newly implemented web service provides instant access to the data for programmers via a SOAP (Simple Object Access Protocol) interface. The BRENDA data can be downloaded in the form of a text file from the beginning of 2007.


Sujet(s)
Bases de données de protéines , Enzymes/composition chimique , Enzymes/physiologie , Animaux , Enzymes/génétique , Génomique , Humains , Internet , Protéines membranaires/composition chimique , Rats , Intégration de systèmes , Interface utilisateur
14.
Nucleic Acids Res ; 32(Database issue): D431-3, 2004 Jan 01.
Article de Anglais | MEDLINE | ID: mdl-14681450

RÉSUMÉ

BRENDA (BRaunschweig ENzyme DAtabase) represents a comprehensive collection of enzyme and metabolic information, based on primary literature. The database contains data from at least 83,000 different enzymes from 9800 different organisms, classified in approximately 4200 EC numbers. BRENDA includes biochemical and molecular information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure, application, engineering, stability, disease, isolation and preparation, links and literature references. The data are extracted and evaluated from approximately 46,000 references, which are linked to PubMed as long as the reference is cited in PubMed. In the past year BRENDA has undergone major changes including a large increase in updating speed with >50% of all data updated in 2002 or in the first half of 2003, the development of a new EC-tree browser, a taxonomy-tree browser, a chemical substructure search engine for ligand structure, the development of controlled vocabulary, an ontology for some information fields and a thesaurus for ligand names. The database is accessible free of charge to the academic community at http://www.brenda. uni-koeln.de.


Sujet(s)
Bases de données de protéines , Enzymes/composition chimique , Enzymes/métabolisme , Animaux , Enzymes/classification , Humains , Mémorisation et recherche des informations , Internet , Ligands , Spécificité d'organe , Conformation des protéines , Transport des protéines , Spécificité du substrat , Terminologie comme sujet
15.
Trends Biochem Sci ; 27(1): 54-6, 2002 Jan.
Article de Anglais | MEDLINE | ID: mdl-11796225

RÉSUMÉ

BRENDA (BRaunschweig ENzyme DAtabase), founded in 1987 by Dietmar Schomburg, is a comprehensive protein function database, containing enzymatic and metabolic information extracted from the primary literature. Presently, the database holds data on more than 40 000 enzymes and 4460 different organisms, and includes information about enzyme-ligand relationships with numerous chemical compounds. The collection of molecular and biochemical information in BRENDA provides a fundamental resource for research in biotechnology, pharmacology, medicinal diagnostics, enzyme mechanics, and metabolism. BRENDA is accessible free of charge to the academic community at http://www.brenda.uni-koeln.de/; commercial users need a license available from http://www.science-factory.com/


Sujet(s)
Bases de données factuelles , Enzymes/composition chimique , Animaux , Humains
16.
Nucleic Acids Res ; 30(1): 47-9, 2002 Jan 01.
Article de Anglais | MEDLINE | ID: mdl-11752250

RÉSUMÉ

BRENDA is a comprehensive relational database on functional and molecular information of enzymes, based on primary literature. The database contains information extracted and evaluated from approximately 46 000 references, holding data of at least 40 000 different enzymes from more than 6900 different organisms, classified in approximately 3900 EC numbers. BRENDA is an important tool for biochemical and medical research covering information on properties of all classified enzymes, including data on the occurrence, catalyzed reaction, kinetics, substrates/products, inhibitors, cofactors, activators, structure and stability. All data are connected to literature references which in turn are linked to PubMed. The data and information provide a fundamental tool for research of enzyme mechanisms, metabolic pathways, the evolution of metabolism and, furthermore, for medicinal diagnostics and pharmaceutical research. The database is a resource for data of enzymes, classified according to the EC system of the IUBMB Enzyme Nomenclature Committee, and the entries are cross-referenced to other databases, i.e. organism classification, protein sequence, protein structure and literature references. BRENDA provides an academic web access at http://www.brenda.uni-koeln.de.


Sujet(s)
Bases de données de protéines , Enzymes/composition chimique , Enzymes/métabolisme , Animaux , Enzymes/physiologie , Humains , Mémorisation et recherche des informations , Internet , Ligands
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