What is a metabolite
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A metabolite is the intermediate end product of metabolism. The term "metabolite" is usually restricted to small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, catalytic activity of their own (usually as a cofactor to an enzyme), defense, and interactions with other organisms (e.g. pigments, odorants, and pheromones). A primary metabolite is directly involved in normal "growth", development, and reproduction. Ethylene is an example of a primary metabolite produced in large-scale by industrial microbiology. A secondary metabolite is not directly involved in those processes, but usually has an important ecological function. Examples include antibiotics and pigments such as resins and terpenes etc. Some antibiotics use primary metabolites as precursors, such as actinomycin which is created from the primary metabolite, tryptophan. Some sugars are metabolites, such as fructose or glucose, which are both present in the metabolic pathways.
Metabolite
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Metabolites are the intermediates and products of metabolism. Within the context of metabolomics, a metabolite is usually defined as any molecule less than 1 kDa in size. However, there are exceptions to this depending on the sample and detection method. For example, macromolecules such as lipoproteins and albumin are reliably detected in NMR-based metabolomics studies of blood plasma. In plant-based metabolomics, it is common to refer to "primary" and "secondary" metabolites. A primary metabolite is directly involved in the normal growth, development, and reproduction. A secondary metabolite is not directly involved in those processes, but usually has important ecological function. Examples include antibiotics and pigments. By contrast, in human-based metabolomics, it is more common to describe metabolites as being either endogenous (produced by the host organism) or exogenous. Metabolites of foreign substances such as drugs are termed xenometabolites.
Metabolomics
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To qualify as a metabolite, or to be considered to be part of the metabolome, a small molecule must typically have a molecular weight <1500 Da. This means that molecules such as glycolipids, polysaccharides, short peptides (<14 amino acids) and small oligonucleotides (<5 bases) can be regarded as metabolites or constituents of the metabolome. On the other hand, very large macromolecules such as proteins, messenger RNA, ribosomal RNA, microRNA and DNA are definitely not metabolites and are not considered to be part of the metabolome. The study of the metabolome is called metabolomics.
Metabolome
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Secondary metabolites are organic compounds produced by bacteria, fungi, or plants which are not directly involved in the normal growth, development, or reproduction of the organism. Unlike primary metabolites, absence of secondary metabolites does not result in immediate death, but rather in long-term impairment of the organism's survivability, fecundity, or aesthetics, or perhaps in no significant change at all. Specific secondary metabolites are often restricted to a narrow set of species within a phylogenetic group. Secondary metabolites often play an important role in plant defense against herbivory and other interspecies defenses. Humans use secondary metabolites as medicines, flavorings, pigments, and recreational drugs.
Secondary metabolite
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Metabolome refers to the complete set of small-molecule metabolites (such as metabolic intermediates, hormones and other signaling molecules, and secondary metabolites) to be found within a biological sample, such as a single organism. The word was coined in analogy with transcriptomics and proteomics; like the transcriptome and the proteome, the metabolome is dynamic, changing from second to second. Although the metabolome can be defined readily enough, it is not currently possible to analyse the entire range of metabolites by a single analytical method. The first metabolite database(called METLIN) for searching m/z values from mass spectrometry data was developed by scientists at The Scripps Research Institute in 2005. In January 2007, scientists at the University of Alberta and the University of Calgary completed the first draft of the human metabolome. The Human Metabolome Database (HMDB) is perhaps the most extensive public metabolomic spectral database to date. The HMDB stores more than 40,000 different metabolite entries. They catalogued approximately 2500 metabolites, 1200 drugs and 3500 food components that can be found in the human body, as reported in the literature. This information, available at the Human Metabolome Database (www.hmdb.ca) and based on analysis of information available in the current scientific literature, is far from complete. In contrast, much more is known about the metabolomes of other organisms. For example, over 50,000 metabolites have been characterized from the plant kingdom, and many thousands of metabolites have been identified and/or characterized from single plants.
Metabolomics
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Similarly to DNA and proteins, metabolites are prone to damage, which can occur chemically or through enzyme promiscuity. Much less is known about metabolite damage than about DNA and protein damage, in part due to the huge variety and number of damage-prone metabolites.
Many metabolites are chemically reactive and unstable, and thus prone to chemical damage. In general, any reaction that occurs "in vitro" under physiological conditions can also occur "in vivo". Some metabolites are so reactive that their half-life in a cell is measured in minutes. For example, the glycolytic intermediate 1,3-bisphosphoglyceric acid has a half-life of 27 minutes "in vivo". Typical types of chemical damage reactions that can occur to metabolites are racemization, rearrangement, elimination, photodissociation, addition, and condensation.
Metabolite damage
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The Human Metabolome Database is a freely available, open-access database containing detailed data on more than 40,000 metabolites that have already been identified or are likely to be found in the human body. The HMDB contains three kinds of information: 1) chemical information, 2) clinical information, and 3) biochemical information. The chemical data includes >40,000 metabolite structures with detailed descriptions, extensive chemical classifications, synthesis information and observed/calculated chemical properties. It also contains nearly 10,000 experimentally measured NMR, GC-MS and LC/MS spectra from more than 1100 different metabolites. The clinical information includes data on >10,000 metabolite-biofluid concentrations, metabolite concentration information on more than 600 different human diseases and pathway data for more than 200 different inborn errors of metabolism. The biochemical information includes nearly 6000 protein (and DNA) sequences and more than 5000 biochemical reactions that are linked to these metabolite entries. The HMDB supports a wide variety of online queries including text searches, chemical structure searches, sequence similarity searches and spectral similarity searches. This makes it particularly useful for metabolomic researchers who are attempting to identify or understand metabolites in clinical metabolomic studies. The first version of the HMDB was released in Jan. 1 2007 and was compiled by scientists at the University of Alberta and the University of Calgary. At that time they reported data on 2,500 metabolites, 1,200 drugs and 3,500 food components. Since then these scientists have greatly expanded the collection. The latest version of the HMDB (version 3.5) contains >16,000 endogenous metabolites, >1500 drugs and >22,000 food constituents or food metabolites.
Metabolome
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The MSEA web server is a freely available web server for performing metabolite set enrichment analysis on human or mammalian metabolomics data. The required input is either a list of compound names or compound names and concentrations. The output is a set of graphs and tables with embedded hyperlinks to the pertinent pathway images and descriptors. The Metabolite Set Enrichment Analysis offered by the web server is based on a curated library of more 5000 predefined metabolite sets covering various human metabolic pathways (nearly 100), hundreds of human disease states (in 3 different biofluids), human biofluid and tissue locations as well as human SNP-metabolite associations (4500 different SNP associations). MSEA also allows users to upload custom metabolite sets for more specialized analysis (such as non-mammalian MSEA work). Three different enrichment analyses are supported by the server: 1) overrepresentation analysis (ORA); 2) single sample profiling (SSP) and 3) quantitative enrichment analysis (QEA). ORA analysis only needs a list of compound names. SSP and QEA need both compound names and their concentrations. Workflows, examples and other screenshot tutorials on how to use the server are available on the MSEA website. The MSEA server also offers a number of other functions including the conversion between metabolite common names, synonyms, and major database identifiers.
Metabolite Set Enrichment Analysis
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Secondary metabolites are essentially low molecular weight compounds, sometimes having complex structures, that are not essential for the normal processes of growth, development, or reproduction. They function in processes as diverse as immunity, anti-herbivory, pollinator attraction, communication between plants, maintaining symbiotic associations with soil flora, or enhancing the rate of fertilization, and hence are significant from the evo-devo perspective. Secondary metabolites are structurally and functionally diverse, and it is estimated that hundreds of thousands of enzymes might be involved in the process of producing them, with about 15–25% of the genome coding for these enzymes, and every species having its unique arsenal of secondary metabolites. Many of these metabolites, such as salicylic acid are of medical significance to humans.
Evolutionary history of plants
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The metabolome reflects the interaction between an organism’s genome and its environment. As a result, an organism’s metabolome can serve as an excellent probe of its phenotype (i.e. the product of its genotype and its environment). Metabolites can be measured (identified, quantified or classified) using a number of different technologies including NMR spectroscopy and mass spectrometry. Most mass spectrometry (MS) methods must be coupled to various forms of liquid chromatography (LC), gas chromatography (GC) or capillary electrophoresis (CE) to facilitate compound separation. Each method is typically able to identify or characterize 50-5000 different metabolites or metabolite “features” at a time, depending on the instrument or protocol being used. See Figure 2 for an illustration of the relationship between different analytical methods and their sensitivity. Currently it is not possible to analyze the entire range of metabolites by a single analytical method.
Metabolome