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Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA–Binding Domain
Transcription factors have two functional constraints on their evolution: (1) their binding sites must have enough information to be distinguishable from all other sequences in the genome, and (2) they must bind these sites with an affinity that appropriately modulates the rate of transcription. Sin...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315485/ https://www.ncbi.nlm.nih.gov/pubmed/22496663 http://dx.doi.org/10.1371/journal.pgen.1002614 |
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author | Shultzaberger, Ryan K. Maerkl, Sebastian J. Kirsch, Jack F. Eisen, Michael B. |
author_facet | Shultzaberger, Ryan K. Maerkl, Sebastian J. Kirsch, Jack F. Eisen, Michael B. |
author_sort | Shultzaberger, Ryan K. |
collection | PubMed |
description | Transcription factors have two functional constraints on their evolution: (1) their binding sites must have enough information to be distinguishable from all other sequences in the genome, and (2) they must bind these sites with an affinity that appropriately modulates the rate of transcription. Since both are determined by the biophysical properties of the DNA–binding domain, selection on one will ultimately affect the other. We were interested in understanding how plastic the informational and regulatory properties of a transcription factor are and how transcription factors evolve to balance these constraints. To study this, we developed an in vivo selection system in Escherichia coli to identify variants of the helix-turn-helix transcription factor MarA that bind different sets of binding sites with varying degrees of degeneracy. Unlike previous in vitro methods used to identify novel DNA binders and to probe the plasticity of the binding domain, our selections were done within the context of the initiation complex, selecting for both specific binding within the genome and for a physiologically significant strength of interaction to maintain function of the factor. Using MITOMI, quantitative PCR, and a binding site fitness assay, we characterized the binding, function, and fitness of some of these variants. We observed that a large range of binding preferences, information contents, and activities could be accessed with a few mutations, suggesting that transcriptional regulatory networks are highly adaptable and expandable. |
format | Online Article Text |
id | pubmed-3315485 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-33154852012-04-11 Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA–Binding Domain Shultzaberger, Ryan K. Maerkl, Sebastian J. Kirsch, Jack F. Eisen, Michael B. PLoS Genet Research Article Transcription factors have two functional constraints on their evolution: (1) their binding sites must have enough information to be distinguishable from all other sequences in the genome, and (2) they must bind these sites with an affinity that appropriately modulates the rate of transcription. Since both are determined by the biophysical properties of the DNA–binding domain, selection on one will ultimately affect the other. We were interested in understanding how plastic the informational and regulatory properties of a transcription factor are and how transcription factors evolve to balance these constraints. To study this, we developed an in vivo selection system in Escherichia coli to identify variants of the helix-turn-helix transcription factor MarA that bind different sets of binding sites with varying degrees of degeneracy. Unlike previous in vitro methods used to identify novel DNA binders and to probe the plasticity of the binding domain, our selections were done within the context of the initiation complex, selecting for both specific binding within the genome and for a physiologically significant strength of interaction to maintain function of the factor. Using MITOMI, quantitative PCR, and a binding site fitness assay, we characterized the binding, function, and fitness of some of these variants. We observed that a large range of binding preferences, information contents, and activities could be accessed with a few mutations, suggesting that transcriptional regulatory networks are highly adaptable and expandable. Public Library of Science 2012-03-29 /pmc/articles/PMC3315485/ /pubmed/22496663 http://dx.doi.org/10.1371/journal.pgen.1002614 Text en Shultzaberger et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Shultzaberger, Ryan K. Maerkl, Sebastian J. Kirsch, Jack F. Eisen, Michael B. Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA–Binding Domain |
title | Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA–Binding Domain |
title_full | Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA–Binding Domain |
title_fullStr | Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA–Binding Domain |
title_full_unstemmed | Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA–Binding Domain |
title_short | Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA–Binding Domain |
title_sort | probing the informational and regulatory plasticity of a transcription factor dna–binding domain |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315485/ https://www.ncbi.nlm.nih.gov/pubmed/22496663 http://dx.doi.org/10.1371/journal.pgen.1002614 |
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