The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space.
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| Title: | The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space. |
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| Authors: | Silva‐Rocha, Rafael1, Lorenzo, Víctor1 |
| Source: | Environmental Microbiology. Jan2013, Vol. 15 Issue 1, p271-286. 16p. |
| Subjects: | Pseudomonas putida, Bacterial proteins, Bacterial ecology, Bacterial genetics, Cellular signal transduction, Bacterial metabolism, Gene expression in bacteria, Algorithms |
| 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. [ABSTRACT FROM AUTHOR] |
| Copyright of Environmental Microbiology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Text: Availability: 0 |
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| Header | DbId: egs DbLabel: Engineering Source An: 84578160 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Silva‐Rocha%2C+Rafael%22">Silva‐Rocha, Rafael</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Lorenzo%2C+Víctor%22">Lorenzo, Víctor</searchLink><relatesTo>1</relatesTo> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Environmental+Microbiology%22">Environmental Microbiology</searchLink>. Jan2013, Vol. 15 Issue 1, p271-286. 16p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Pseudomonas+putida%22">Pseudomonas putida</searchLink><br /><searchLink fieldCode="DE" term="%22Bacterial+proteins%22">Bacterial proteins</searchLink><br /><searchLink fieldCode="DE" term="%22Bacterial+ecology%22">Bacterial ecology</searchLink><br /><searchLink fieldCode="DE" term="%22Bacterial+genetics%22">Bacterial genetics</searchLink><br /><searchLink fieldCode="DE" term="%22Cellular+signal+transduction%22">Cellular signal transduction</searchLink><br /><searchLink fieldCode="DE" term="%22Bacterial+metabolism%22">Bacterial metabolism</searchLink><br /><searchLink fieldCode="DE" term="%22Gene+expression+in+bacteria%22">Gene expression in bacteria</searchLink><br /><searchLink fieldCode="DE" term="%22Algorithms%22">Algorithms</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: 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. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Environmental Microbiology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1111/1462-2920.12014 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 16 StartPage: 271 Subjects: – SubjectFull: Pseudomonas putida Type: general – SubjectFull: Bacterial proteins Type: general – SubjectFull: Bacterial ecology Type: general – SubjectFull: Bacterial genetics Type: general – SubjectFull: Cellular signal transduction Type: general – SubjectFull: Bacterial metabolism Type: general – SubjectFull: Gene expression in bacteria Type: general – SubjectFull: Algorithms Type: general Titles: – TitleFull: The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Silva‐Rocha, Rafael – PersonEntity: Name: NameFull: Lorenzo, Víctor IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 01 Text: Jan2013 Type: published Y: 2013 Identifiers: – Type: issn-print Value: 14622912 Numbering: – Type: volume Value: 15 – Type: issue Value: 1 Titles: – TitleFull: Environmental Microbiology Type: main |
| ResultId | 1 |
