Chlamydomonas reinhardtii is a single-cell green alga about 10 micrometres in diameter that swims with two flagella. It has a cell wall made of hydroxyproline-rich glycoproteins, a large cup-shaped chloroplast, a large pyrenoid, and an eyespot apparatus that senses light.
The metabolome refers to the complete set of small-molecule chemicals found within a biological sample. The biological sample can be a cell, a cellular organelle, an organ, a tissue, a tissue extract, a biofluid or an entire organism. The small molecule chemicals found in a given metabolome may include both endogenous metabolites that are naturally produced by an organism as well as exogenous chemicals that are not naturally produced by an organism.
BRENDA is the world's most comprehensive online database for functional, biochemical and molecular biological data on enzymes, metabolites and metabolic pathways. It contains data on the properties, function and significance of all enzymes classified by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology (IUBMB). As ELIXIR Core Data Resource and Global Core Biodata Resource, BRENDA is considered a data resource of critical importance to the international life sciences research community. The database compiles a representative overview of enzymes and metabolites using current research data from primary scientific literature and thus serves the purpose of facilitating information retrieval for researchers. BRENDA is subject to the terms of the Creative Commons license, is accessible worldwide and can be used free of charge. As one of the digital resources of the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, BRENDA is part of the integrated biodata infrastructure DSMZ Digital Diversity.
A metabolic network is the complete set of metabolic and physical processes that determine the physiological and biochemical properties of a cell. As such, these networks comprise the chemical reactions of metabolism, the metabolic pathways, as well as the regulatory interactions that guide these reactions.
Metabolic network modelling, also known as metabolic network reconstruction or metabolic pathway analysis, allows for an in-depth insight into the molecular mechanisms of a particular organism. In particular, these models correlate the genome with molecular physiology. A reconstruction breaks down metabolic pathways into their respective reactions and enzymes, and analyzes them within the perspective of the entire network. In simplified terms, a reconstruction collects all of the relevant metabolic information of an organism and compiles it in a mathematical model. Validation and analysis of reconstructions can allow identification of key features of metabolism such as growth yield, resource distribution, network robustness, and gene essentiality. This knowledge can then be applied to create novel biotechnology.
KEGG is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development.
In biochemistry, flux balance analysis (FBA) is a mathematical method for simulating the metabolism of cells or entire unicellular organisms, such as E. coli or yeast, using genome-scale reconstructions of metabolic networks. Genome-scale reconstructions describe all the biochemical reactions in an organism based on its entire genome. These reconstructions model metabolism by focusing on the interactions between metabolites, identifying which metabolites are involved in the various reactions taking place in a cell or organism, and determining the genes that encode the enzymes which catalyze these reactions. In comparison to traditional methods of modeling, FBA is less intensive in terms of the input data required for constructing the model. Simulations performed using FBA are computationally inexpensive and can calculate steady-state metabolic fluxes for large models in a few seconds on modern personal computers. The related method of metabolic pathway analysis seeks to find and list all possible pathways between metabolites.
Phosphoribosyl pyrophosphate (PRPP) is a pentose phosphate. It is a biochemical intermediate in the formation of purine nucleotides via inosine-5-monophosphate, as well as in pyrimidine nucleotide formation. Hence it is a building block for DNA and RNA. The vitamins thiamine and cobalamin, and the amino acid tryptophan also contain fragments derived from PRPP. It is formed from ribose 5-phosphate (R5P) by the enzyme ribose-phosphate diphosphokinase:
The hisB gene, found in the enterobacteria, in Campylobacter jejuni and in Xylella/Xanthomonas encodes a protein involved in catalysis of two step in histidine biosynthesis, namely the bifunctional Imidazoleglycerol-phosphate dehydratase/histidinol-phosphatase.
In bioinformatics, EcoCyc is a biological database for the bacterium Escherichia coli K-12. The EcoCyc project performs literature-based curation of the E. coli genome, and of E. coli transcriptional regulation, transporters, and metabolic pathways. EcoCyc contains written summaries of E. coli genes, distilled from over 36,000 scientific articles. EcoCyc is also a description of the genome and cellular networks of E. coli that supports scientists to carry out computational analyses.
The MetaCyc database is one of the largest metabolic pathways and enzymes databases currently available. The data in the database is manually curated from the scientific literature, and covers all domains of life. MetaCyc has extensive information about chemical compounds, reactions, metabolic pathways and enzymes. The data have been curated from more than 58,000 publications.
Aldolase A deficiency is an autosomal recessive metabolic disorder resulting in a deficiency of the enzyme aldolase A; the enzyme is found predominantly in red blood cells and muscle tissue. The deficiency may lead to hemolytic anaemia as well as myopathy associated with exercise intolerance and rhabdomyolysis in some cases.
Phosphoribosylamine (PRA) is a biochemical intermediate in the formation of purine nucleotides via inosine-5-monophosphate, and hence is a building block for DNA and RNA. The vitamins thiamine and cobalamin also contain fragments derived from PRA.
Nitrite oxidoreductase is an enzyme involved in nitrification. It is the last step in the process of aerobic ammonia oxidation, which is carried out by two groups of nitrifying bacteria: ammonia oxidizers such as Nitrosospira, Nitrosomonas, and Nitrosococcus convert ammonia to nitrite, while nitrite oxidizers such as Nitrobacter and Nitrospira oxidize nitrite to nitrate. NXR is responsible for producing almost all nitrate found in nature.
5′-Phosphoribosyl-5-aminoimidazole is a biochemical intermediate in the formation of purine nucleotides via inosine-5-monophosphate, and hence is a building block for DNA and RNA. The vitamins thiamine and cobalamin also contain fragments derived from AIR. It is an intermediate in the adenine pathway and is synthesized from 5′-phosphoribosylformylglycinamidine by AIR synthetase.
Methanocaldococcussp. FS406-22 is an archaea in the genus Methanocaldococcus. It is an anaerobic, piezophilic, diazotrophic, hyperthermophilic marine archaeon. This strain is notable for fixing nitrogen at the highest known temperature of nitrogen fixers recorded to date. The 16S rRNA gene of Methanocaldococcus sp. FS406-22, is almost 100% similar to that of Methanocaldococcus jannaschii, a non-nitrogen fixer.
Chlorophyllide a and Chlorophyllide b are the biosynthetic precursors of chlorophyll a and chlorophyll b respectively. Their propionic acid groups are converted to phytyl esters by the enzyme chlorophyll synthase in the final step of the pathway. Thus the main interest in these chemical compounds has been in the study of chlorophyll biosynthesis in plants, algae and cyanobacteria. Chlorophyllide a is also an intermediate in the biosynthesis of bacteriochlorophylls.
Peter D. Karp is director of the Bioinformatics Research Group at SRI International in Menlo Park, California. Karp leads the development of the BioCyc database collection. BioCyc databases combine genome, metabolic pathway, and regulatory information for thousands of organisms.
SoyBase is a database created by the United States Department of Agriculture. It contains genetic information about soybeans. It includes genetic maps, information about Mendelian genetics and molecular data regarding genes and sequences. It was started in 1990 and is freely available to individuals and organizations worldwide.
