Metabolic pathways, reconstruction

Saulnier, D.M., Santos, E, Roos, S., Mistretta, T.-A. et al (2011) Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features. PLoS One, 6, el8783. 

Besides the engineering of S. cerevisiae for organic acid production, through metabolic engineering it is possible to reconstruct entire pathways. In 1994, Yamano et al. [163] reported the reconstruction of a complete secondary metabolic pathway in S. cerevisiae, resulting in the ability of the yeast to produce p-carotene and lycopene. Carotenoids are a class of pigments used in the food industry and, due to their antioxidant properties, they have wide commercial interest. The biosynthesis of these compounds does naturally not occur in S. cerevisiae and to allow... 

Metabolic pathways have been illustrated using simple diagrams since before the human genome project and related bioinformatics projects had begun. With the involvement of computer science techniques, however, systematic approaches to modeling metabolic pathways have progressed quickly, with various aims that range from metabolite analyses to pathway prediction and reconstruction (1-3). Systems analysis has come to incorporate... 

In fact, fermentation is both the oldest and newest type of catalytic processing. In the very old days— back to several thousand years BC— beer, bread and winemaking were t) ical fermentation processes. In the present, modern recombinant DNA technology allows us to reconstruct the cell factories, i.e. the metabolic pathways, and so to develop novel multi-step conversions by fermentation that are not available in nature. 

Allow the metabolic reconstruction of microbial genomes. EcoCyc provides detailed annotation on 946 metabolic reactions comprising 139 distinct metabolic pathways. EcoCyc also includes information on the signal-transduction pathways, enzymes, and transport proteins of E. coli. MetaCyc describes 3,786 pathways and enzymes of many different organisms with a primary microbial focus. 

APPLICATION OF COMPARATIVE GENOMICS—RECONSTRUCTION OF METABOLIC PATHWAYS... 

The representation of each substance at an atomic rather than a molecular level allows focus on structural elements of each metabolite. Results of automated pathway reconstruction are based on computed movements in the location of each atom by the tracing engine of the software. The construction of a mapping database, which enables atomic tracers and search functions for certain structural elements, serves to close the gap between pathway databases and computer simulations. Though the coverage of the mapping database is important for reliable reconstruction, once a reasonable set of metabolome data from secondary metabolism is obtained, hypothetical pathways and relationships can be computed... 

Bolten, C.J., Heinzle, E., Muller, R., and Wittmann, C. (2009) Investigation of the central carbon metabolism of Sorangium cellulosum metabolic network reconstruction and quantification of pathway fluxes. /. Microbiol. Biotechnol, 19 (1), 23-36. 

Finally, three strains of Lactobacillus reuteri have been used for GEMM reconstrac-tion. Lactobacillus reuteri JCMl 12 had been used for medium optimization to enhance vitamin B12 biosynthesis by insertion of the biosynthetic pathway from Lactobacillus plantarum WCFSl (Santos et al 2008). Furthermore, two isolates derived from breast milk have been used for metabolic model reconstructions (Saulnier et al 2011). Lactobacillus reuteri strain 55730 has been identified as an important probiotic strain, and hence efforts were made to identify its functional properties via the integration of omics data, in particular, the amino acid biosynthesis capacity and vitamin production were detailed thanks to the model and proposed as part of traits enhancing probiotic effects. Such study represents an important step toward a metagenome-scale model and its application in industrial fermentations (Branco Dos Santos, De Vos, Teusink, 2013). 

---