Combining Genomics, Metabolome Analysis, and Biochemical Modelling to Understand Metabolic Networks

By Oliver Fiehn. Comparative and Functional Genomics, 2001

876 citations recorded by the source corpus.

Now that complete genome sequences are available for a variety of organisms, the elucidation of gene functions involved in metabolism necessarily includes a better understanding of cellular responses upon mutations on all levels of gene products, mRNA, proteins, and metabolites. Such progress is essential since the observable properties of organisms – the phenotypes – are produced by the genotype in juxtaposition with the environment. Whereas much has been done to make mRNA and protein profiling possible, considerably less effort has been put into profiling the end products of gene expression, metabolites. To date, analytical approaches have been aimed primarily at the accurate quantification of a number of pre-defined target metabolites, or at producing fingerprints of metabolic changes without individually determining metabolite identities. Neither of these approaches allows the formation of an in-depth understanding of the biochemical behaviour within metabolic networks. Yet, by carefully choosing protocols for sample preparation and analytical techniques, a number of chemically different classes of compounds can be quantified simultaneously to enable such understanding. In this review, the terms describing various metabolite-oriented approaches are given, and the differences among these approaches are outlined. Metabolite target analysis, metabolite profiling, metabolomics, and metabolic fingerprinting are considered. For each approach, a number of examples are given, and potential applications are discussed.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/06d8ee888fdb59d0784931f329d3d1c1ac06a41a

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Citations in the corpus

Targeted Metabolomics (2012, background): “…comprehensive metabolomic evaluation include the size of the metabolome, which is estimated to range from ∼600 metabolites in S. cerevisiae (Forster et al., 2003) to ∼200,000 metabolites in plants (Fiehn, 2001), and the dynamic range of metabolite concentrations, which spans across many…”
Plant Metabolomics: The Missing Link in Functional Genomics Strategies (2002, background): “Approximately 50,000 different compounds have been elucidated in plants (De Luca and St. Pierre, 2000), and it is predicted that the final figure for the plant kingdom will approach or even exceed 200,000 (Pichersky and Gang, 2000; Fiehn, 2001, 2002).”
The use of metabolomics to dissect plant responses to abiotic stresses (2012, neutral): “small molecules in a biological system [1].”
Classification of olive oils according to geographical origin by using 1H NMR fingerprinting combined with multivariate analysis (2012, methodology): “More recently, NMR has been used for the prediction of the olive oil geographical origin using a fingerprinting approach (Fiehn, 2001), where the spectra are used as a whole (fingerprint) without assigning particular resonances and thus obtaining a comprehensive, multivariate, description of the ana”
Halophyte Improvement for a Salinized World (2010, background): “, 2007), sample preparation and data acquisition and interpretation (Fiehn, 2001), metabolic diversity (Harrigan et al.”
Metabolomics by numbers: acquiring and understanding global metabolite data. (2004, background): “provenance of either their biological relevance or origin [ 70 ].”
Metabolomics technology and bioinformatics (2006, background): “The first implication here is that, not knowing a priori which metabolites are expected to be altered, the profiles then need to be as comprehensible as possible; the second implication is that studying the metabolite profiles of a number of mutants might lead to the discovery of the underlying meta”
Innovation: Metabolomics: the apogee of the omics trilogy (2012, background): “Additionally, contemporary metabolic profiling experiments have the advantage of being complemented by genomic sequencing and proteomic screenin”
Metabolomic database annotations via query of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm (2006, background): “Background Metabolomics seeks to identify and quantify all metabolites in a given biological context [1].”
Secondary Metabolites as Plant Traits: Current Assessment and Future Perspectives (2002, background): “In metabolomic approaches, any bias against certain classes of metabolites is to be avoided (Fiehn, 2001; Fiehn et al., 2001).”