Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 409344
Title The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms
Author(s) Silva-Rocha, R.; Tamames, J.; Martins Dos Santos, V.A.P.; Lorenzo, V. de
Source Environmental Microbiology 13 (2011)9. - ISSN 1462-2912 - p. 2389 - 2402.
DOI http://dx.doi.org/10.1111/j.1462-2920.2011.02455.x
Department(s) Systems and Synthetic Biology
VLAG
Publication type Refereed Article in a scientific journal
Publication year 2011
Keyword(s) pseudomonas-putida kt2440 - integration host factor - sigma(54)-dependent promoter pu - scale metabolic reconstruction - upper-pathway operon - tol plasmid pww0 - aromatic-compounds - transcriptional regulation - escherichia-coli - rna-polymerase
Abstract The regulatory and metabolic networks that rule biodegradation of pollutants by environmental bacteria are wired to the rest of the cellular physiology through both transcriptional factors and intermediary signal molecules. In this review, we examine some formalisms for describing catalytic/regulatory circuits of this sort and advocate the adoption of Boolean logic for combining transcriptional and enzymatic occurrences in the same biological system. As an example, we show how known regulatory and metabolic actions that bring about biodegradation of m-xylene by Pseudomonas putida mt-2 can be represented as clusters of binary operations and then reconstructed as a digital network. Despite the many simplifications, Boolean tools still capture the gross behaviour of the system even in the absence of kinetic constants determined experimentally. On this basis, we argue that still with a limited volume of data binary formalisms allow us to penetrate the raison d'être of extant regulatory and metabolic architectures
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