title: The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space.
abstract: The TOL system encoded by plasmid pWW0 of Pseudomonas putida mt-2 is able to sense a large number of both exogenous and endogenous signals as inputs for the genetic and metabolic circuit that determines the biodegradation of m-xylene. However, whether the enormous combinatorial space of inputs is translated into an equally variable response landscape or is processed into very few outcomes remains unclear. To address this question, we set out to define the number of states that can be obtained by a network of a given set of genes under the control of a specified regulatory circuit that is exposed to all possible combinations of inputs. To this end, the TOL network and its regulatory wiring were formalized as a synchronous logic Boolean circuit that had 10 signals (i.e. pathway substrates, temperature, sugars, amino acids, metabolic regimes and global regulators) as possible inputs. The analysis of the attractors of the circuit using a satisfiability (SAT) algorithm revealed that only eight transcriptional states are reached in response to the 1024 possible combinations of stimuli. The experimental validation resulted in a refinement of the model through the addition of a previously unknown interaction that controls the meta catabolic pathway. The full induction of the two xyl operons occurred with only 1.6% of the input combinations, which suggests that the architecture of the network allows the expression of the xyl genes only under a very narrow range of conditions. These data not only explain much of the unusual layout of the TOL circuit but also strengthen the view of the regulatory circuits of environmental bacteria as digital decision-making devices.
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: Víctor
authors.initials: V
authors.lastname: de Lorenzo
mesh_terms: D001673:Biodegradation, Environmental; D004777:Environment; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D005798:Genes, Bacterial / Q000235:genetics*; D008954:Models, Biological; D010957:Plasmids / Q000235:genetics; D016958:Pseudomonas putida / Q000235:genetics* / Q000378:metabolism*; D015398:Signal Transduction; D012989:Soil Pollutants / Q000378:metabolism; D014992:Xylenes / Q000378:metabolism
chemical_list: D012989:Soil Pollutants; D014992:Xylenes; C031285:3-xylene