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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC3315485?pdf=render |
| _version_ | 1818039581631578112 |
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| author | Ryan K Shultzaberger Sebastian J Maerkl Jack F Kirsch Michael B Eisen |
| author_facet | Ryan K Shultzaberger Sebastian J Maerkl Jack F Kirsch Michael B Eisen |
| author_sort | Ryan K Shultzaberger |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-10T08:00:55Z |
| format | Article |
| id | doaj.art-6d7ffe701564450b81f475328a66a884 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-10T08:00:55Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-6d7ffe701564450b81f475328a66a8842022-12-22T01:56:47ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042012-01-0183e100261410.1371/journal.pgen.1002614Probing the informational and regulatory plasticity of a transcription factor DNA-binding domain.Ryan K ShultzabergerSebastian J MaerklJack F KirschMichael B EisenTranscription 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.http://europepmc.org/articles/PMC3315485?pdf=render |
| spellingShingle | Ryan K Shultzaberger Sebastian J Maerkl Jack F Kirsch Michael B Eisen Probing the informational and regulatory plasticity of a transcription factor DNA-binding domain. PLoS Genetics |
| 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 |
| url | http://europepmc.org/articles/PMC3315485?pdf=render |
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