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

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Title: The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms.
Authors: Silva-Rocha, Rafael1, Tamames, Javier1, dos Santos, Vitor Martins2, de Lorenzo, Víctor1
Source: Environmental Microbiology. Sep2011, Vol. 13 Issue 9, p2389-2402. 14p. 5 Diagrams.
Subjects: Bacteria, Microbial ecology, Pollutants, Biodegradation, Cell physiology, Transcription factors, Cellular signal transduction, Bacterial metabolism
Abstract: Summary 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. [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.)
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  Data: The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms.
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  Data: <searchLink fieldCode="AR" term="%22Silva-Rocha%2C+Rafael%22">Silva-Rocha, Rafael</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Tamames%2C+Javier%22">Tamames, Javier</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22dos+Santos%2C+Vitor+Martins%22">dos Santos, Vitor Martins</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22de+Lorenzo%2C+Víctor%22">de Lorenzo, Víctor</searchLink><relatesTo>1</relatesTo>
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  Data: <searchLink fieldCode="JN" term="%22Environmental+Microbiology%22">Environmental Microbiology</searchLink>. Sep2011, Vol. 13 Issue 9, p2389-2402. 14p. 5 Diagrams.
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  Data: <searchLink fieldCode="DE" term="%22Bacteria%22">Bacteria</searchLink><br /><searchLink fieldCode="DE" term="%22Microbial+ecology%22">Microbial ecology</searchLink><br /><searchLink fieldCode="DE" term="%22Pollutants%22">Pollutants</searchLink><br /><searchLink fieldCode="DE" term="%22Biodegradation%22">Biodegradation</searchLink><br /><searchLink fieldCode="DE" term="%22Cell+physiology%22">Cell physiology</searchLink><br /><searchLink fieldCode="DE" term="%22Transcription+factors%22">Transcription factors</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>
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  Label: Abstract
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  Data: Summary 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. [ABSTRACT FROM AUTHOR]
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  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.)
PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=egs&AN=65302381
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        Value: 10.1111/j.1462-2920.2011.02455.x
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      – Code: eng
        Text: English
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        PageCount: 14
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        Type: general
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      – SubjectFull: Pollutants
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      – SubjectFull: Transcription factors
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      – SubjectFull: Cellular signal transduction
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            NameFull: dos Santos, Vitor Martins
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              Text: Sep2011
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