Metabolic footprinting

Allen, J. Broadhurst, H. M. Heald, J. K. Rowland, J. J. Oliver, S. G Kell, D. B. High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat. Biotechnol. 2003, 21, 692-696. 

Kaderbhai, N. N. Broadhurst, D. I. Ellis, D. I. Goodacre, R. Kell, D. B. Functional genomics via metabolic footprinting monitoring metabolite secretion by Escherichia coli tryptophan metabolism mutants using FT-IR and direct injection electrospray mass spectrometry. Compar. Func. Genomics 2003, 4, 376-391. 

To use metabolic footprinting as a technique for high-throughput applications, benchmark spectra databases with identified peaks are required so that peak patterns obtained from MS or NMR analysis can be rapidly translated into relevant biological information. Common experimental procedures should, ideally, also be established for metabolite analysis [80] such as those existing in proteomics or transcriptomics. Nevertheless, the scientific community has only recently attempted to achieve these tasks. Several databases for identification of metabolomics signals by MS are now available, for instance, BIGG [81], BioCyc [82], MSlib [83], NIST [84], Metlin [85], and HMDB [86] databases. For a more comprehensive list of resources we refer to the review of Werner and coworkers [68]. 

When this parasite invades the grape-berry, it leaves a characteristic metabolic footprint which has been shown to be closely correlated with the degree of infection and the associated technological problems. Although the correlation is not linear it may nonetheless be modelled using neural networks and thus it is quite possible to express the degree of Botrytis infection in the form of an index. 

The authors found that this "metabolic footprinting" allowed them to... 

Metabolic Footprinting Semiquantitative analysis of the metabolites present in the apoplast. 

Mas S, Villas-Boas SG, Hansen ME, Akesson M, Nielsen J. A comparison of direct infusion MS andGC-MS for metabolic footprinting of yeast mutants. Biotechnol Bioeng. 2007 96(5) 1014-22. doi 10.1002/bit.21194. 

DIRECT INFUSION ESMS OF CRUDE CELL EXTRACTS FOR HIGH-THROUGHPUT CHARACTERIZATIONS—METABOLIC FINGERPRINTING AND FOOTPRINTING... 

FOOTPRINT software tool (www.prodoric.de, [92]). Visualisation is achieved via ProdoNet [93]. Consequently, DNA microarray and proteomic experiments are the experimental validation for our proposals. Furthermore, integration of regulatory and metabolic networks is desired. The identification of limiting steps in protein production and the deduction of molecular optimisation strategies are the major goals in the future. 

The need for novel catalytic processes is clear and, as discussed in Chapter 9, combining catalytic steps into cascade processes, thus obviating the need for isolation of intermediate products, results in a further optimization of both the economics and the environmental footprint of the process. In vivo this amounts to metabolic pathway engineering [20] of the host microorganism (see Chapter 8) and in vitro it constitutes a combination of chemo- and/or biocatalytic steps in series and is referred to as cascade catalysis (see Chapter 9). Metabolic engineering involves, by necessity, renewable raw materials and is a vital component of the future development of renewable feedstocks for fuels and chemicals. 

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