When activators repress and repressors activate: A qualitative analysis of the Shea-Ackers model

Tomáš Gedeon; Konstantin Mischaikow; Kate Patterson; Eliane Traldi

doi:10.1007/s11538-008-9313-6

When activators repress and repressors activate: A qualitative analysis of the Shea-Ackers model

Tomáš Gedeon, Konstantin Mischaikow, Kate Patterson, Eliane Traldi

Research output: Contribution to journal › Article › peer-review

10 Scopus citations

Abstract

The concept of activation in transcriptional regulation is based on the assumption that product mRNA increases monotonically as a function of regulator concentration. We analyze the Shea-Ackers model of transcription and find this assumption to be correct only for the simplest of promoters. We define a new regulatory constant that is a nonlinear combination of association and transcription initiation constants characterizing activation and repression for more complicated promoters. Our results can guide the synthesis of new promoters and lead to a deeper understanding of the constraints guiding the natural promoters evolution.

Original language	English (US)
Pages (from-to)	1660-1683
Number of pages	24
Journal	Bulletin of Mathematical Biology
Volume	70
Issue number	6
DOIs	https://doi.org/10.1007/s11538-008-9313-6
State	Published - Aug 2008

All Science Journal Classification (ASJC) codes

Neuroscience(all)
Immunology
Mathematics(all)
Biochemistry, Genetics and Molecular Biology(all)
Environmental Science(all)
Pharmacology
Agricultural and Biological Sciences(all)
Computational Theory and Mathematics

Keywords

Activator
Mass action kinetics
Prokaryotic transcription
Repressor

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10.1007/s11538-008-9313-6

Cite this

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title = "When activators repress and repressors activate: A qualitative analysis of the Shea-Ackers model",

abstract = "The concept of activation in transcriptional regulation is based on the assumption that product mRNA increases monotonically as a function of regulator concentration. We analyze the Shea-Ackers model of transcription and find this assumption to be correct only for the simplest of promoters. We define a new regulatory constant that is a nonlinear combination of association and transcription initiation constants characterizing activation and repression for more complicated promoters. Our results can guide the synthesis of new promoters and lead to a deeper understanding of the constraints guiding the natural promoters evolution.",

keywords = "Activator, Mass action kinetics, Prokaryotic transcription, Repressor",

author = "Tom{\'a}{\v s} Gedeon and Konstantin Mischaikow and Kate Patterson and Eliane Traldi",

note = "Funding Information: T.G. was partially supported by NSF/NIH grant 0443863, NIH-NCRR grant PR16445, and NSF-CRCNS grant 0515290. K.M. was partially supported by NSF DMS 0443827 and grants from D.O.E. and DARPA. K.P. was supported by NSF/NIH grant 0443863. E.T. was partially supported by NSF DMS 0443827 and CAPES, Brazil.",

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doi = "10.1007/s11538-008-9313-6",

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AU - Gedeon, Tomáš

AU - Mischaikow, Konstantin

AU - Patterson, Kate

AU - Traldi, Eliane

N1 - Funding Information: T.G. was partially supported by NSF/NIH grant 0443863, NIH-NCRR grant PR16445, and NSF-CRCNS grant 0515290. K.M. was partially supported by NSF DMS 0443827 and grants from D.O.E. and DARPA. K.P. was supported by NSF/NIH grant 0443863. E.T. was partially supported by NSF DMS 0443827 and CAPES, Brazil.

PY - 2008/8

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N2 - The concept of activation in transcriptional regulation is based on the assumption that product mRNA increases monotonically as a function of regulator concentration. We analyze the Shea-Ackers model of transcription and find this assumption to be correct only for the simplest of promoters. We define a new regulatory constant that is a nonlinear combination of association and transcription initiation constants characterizing activation and repression for more complicated promoters. Our results can guide the synthesis of new promoters and lead to a deeper understanding of the constraints guiding the natural promoters evolution.

AB - The concept of activation in transcriptional regulation is based on the assumption that product mRNA increases monotonically as a function of regulator concentration. We analyze the Shea-Ackers model of transcription and find this assumption to be correct only for the simplest of promoters. We define a new regulatory constant that is a nonlinear combination of association and transcription initiation constants characterizing activation and repression for more complicated promoters. Our results can guide the synthesis of new promoters and lead to a deeper understanding of the constraints guiding the natural promoters evolution.

KW - Activator

KW - Mass action kinetics

KW - Prokaryotic transcription

KW - Repressor

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When activators repress and repressors activate: A qualitative analysis of the Shea-Ackers model

Abstract

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Keywords

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