The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms

R. Silva-Rocha, J. Tamames, V.A.P. Martins Dos Santos, V. de Lorenzo

Research output: Contribution to journalArticleAcademicpeer-review

29 Citations (Scopus)

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
Original languageEnglish
Pages (from-to)2389-2402
JournalEnvironmental Microbiology
Volume13
Issue number9
DOIs
Publication statusPublished - 2011

Keywords

  • 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

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