Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria
A canonical quantitative view of transcriptional regulation holds that the only role of operator sequence is to set the probability of transcription factor binding, with operator occupancy determining the level of gene expression. In this work, we test this idea by characterizing repression in vivo...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | en_US |
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Elsevier
2014
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| Online Access: | http://hdl.handle.net/1721.1/91648 https://orcid.org/0000-0002-8568-7432 |
| _version_ | 1826201157055283200 |
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| author | Garcia, Hernan G. Boedicker, James Q. Osborne, Melisa Gelles, Jeff Kondev, Jane Phillips, Rob Sanchez Ferro, Alvaro |
| author2 | Massachusetts Institute of Technology. Department of Physics |
| author_facet | Massachusetts Institute of Technology. Department of Physics Garcia, Hernan G. Boedicker, James Q. Osborne, Melisa Gelles, Jeff Kondev, Jane Phillips, Rob Sanchez Ferro, Alvaro |
| author_sort | Garcia, Hernan G. |
| collection | MIT |
| description | A canonical quantitative view of transcriptional regulation holds that the only role of operator sequence is to set the probability of transcription factor binding, with operator occupancy determining the level of gene expression. In this work, we test this idea by characterizing repression in vivo and the binding of RNA polymerase in vitro in experiments where operators of various sequences were placed either upstream or downstream from the promoter in Escherichia coli. Surprisingly, we find that operators with a weaker binding affinity can yield higher repression levels than stronger operators. Repressor bound to upstream operators modulates promoter escape, and the magnitude of this modulation is not correlated with the repressor-operator binding affinity. This suggests that operator sequences may modulate transcription by altering the nature of the interaction of the bound transcription factor with the transcriptional machinery, implying a new layer of sequence dependence that must be confronted in the quantitative understanding of gene expression. |
| first_indexed | 2024-09-23T11:47:07Z |
| format | Article |
| id | mit-1721.1/91648 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T11:47:07Z |
| publishDate | 2014 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | mit-1721.1/916482022-10-01T05:59:27Z Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria Garcia, Hernan G. Boedicker, James Q. Osborne, Melisa Gelles, Jeff Kondev, Jane Phillips, Rob Sanchez Ferro, Alvaro Massachusetts Institute of Technology. Department of Physics Massachusetts Institute of Technology. Research Laboratory of Electronics Sanchez Ferro, Alvaro A canonical quantitative view of transcriptional regulation holds that the only role of operator sequence is to set the probability of transcription factor binding, with operator occupancy determining the level of gene expression. In this work, we test this idea by characterizing repression in vivo and the binding of RNA polymerase in vitro in experiments where operators of various sequences were placed either upstream or downstream from the promoter in Escherichia coli. Surprisingly, we find that operators with a weaker binding affinity can yield higher repression levels than stronger operators. Repressor bound to upstream operators modulates promoter escape, and the magnitude of this modulation is not correlated with the repressor-operator binding affinity. This suggests that operator sequences may modulate transcription by altering the nature of the interaction of the bound transcription factor with the transcriptional machinery, implying a new layer of sequence dependence that must be confronted in the quantitative understanding of gene expression. National Institutes of Health (U.S.) (Grant GM81648) National Institutes of Health (U.S.) (Grant GM43369) 2014-11-20T15:09:19Z 2014-11-20T15:09:19Z 2012-07 2012-05 Article http://purl.org/eprint/type/JournalArticle 22111247 http://hdl.handle.net/1721.1/91648 Garcia, Hernan G., Alvaro Sanchez, James Q. Boedicker, Melisa Osborne, Jeff Gelles, Jane Kondev, and Rob Phillips. “Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria.” Cell Reports 2, no. 1 (July 2012): 150–161. https://orcid.org/0000-0002-8568-7432 en_US http://dx.doi.org/10.1016/j.celrep.2012.06.004 Cell Reports Creative Commons Attribution http://creativecommons.org/licenses/by-nc-nd/3.0/ application/pdf Elsevier Elsevier |
| spellingShingle | Garcia, Hernan G. Boedicker, James Q. Osborne, Melisa Gelles, Jeff Kondev, Jane Phillips, Rob Sanchez Ferro, Alvaro Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria |
| title | Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria |
| title_full | Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria |
| title_fullStr | Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria |
| title_full_unstemmed | Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria |
| title_short | Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria |
| title_sort | operator sequence alters gene expression independently of transcription factor occupancy in bacteria |
| url | http://hdl.handle.net/1721.1/91648 https://orcid.org/0000-0002-8568-7432 |
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