title: The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms.
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.
authors.affiliation: Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, 28049, Spain.
authors.forename: Rafael
authors.initials: R
authors.lastname: Silva-Rocha
authors.forename: Javier
authors.initials: J
authors.lastname: Tamames
authors.forename: Vitor Martins
authors.initials: VM
authors.lastname: dos Santos
authors.forename: Víctor
authors.initials: V
authors.lastname: de Lorenzo
mesh_terms: D001673:Biodegradation, Environmental; D004785:Environmental Pollutants / Q000378:metabolism*; D053263:Gene Regulatory Networks; D053858:Metabolic Networks and Pathways; D008962:Models, Theoretical; D016958:Pseudomonas putida / Q000378:metabolism*; D015398:Signal Transduction; D014157:Transcription Factors / Q000378:metabolism; D014992:Xylenes / Q000378:metabolism*
chemical_list: D004785:Environmental Pollutants; D014157:Transcription Factors; D014992:Xylenes; C031285:3-xylene