Structural basis for higher-order DNA binding by a bacterial transcriptional regulator.
Transcriptional regulation by binding of transcription factors to palindromic sequences in promoter regions is a fundamental process in bacteria. Some transcription factors have multiple dimeric DNA-binding domains, in principle enabling interaction with higher-order DNA structures; however, mechani...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2025-06-01
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| Series: | PLoS Genetics |
| Online Access: | https://doi.org/10.1371/journal.pgen.1011749 |
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| author | Frederik Oskar Graversgaard Henriksen Lan Bich Van Ditlev Egeskov Brodersen Ragnhild Bager Skjerning |
| author_facet | Frederik Oskar Graversgaard Henriksen Lan Bich Van Ditlev Egeskov Brodersen Ragnhild Bager Skjerning |
| author_sort | Frederik Oskar Graversgaard Henriksen |
| collection | DOAJ |
| description | Transcriptional regulation by binding of transcription factors to palindromic sequences in promoter regions is a fundamental process in bacteria. Some transcription factors have multiple dimeric DNA-binding domains, in principle enabling interaction with higher-order DNA structures; however, mechanistic and structural insights into this phenomenon remain limited. The Pseudomonas putida toxin-antitoxin (TA) system Xre-RES has an unusual 4:2 stoichiometry including two potential DNA-binding sites, compatible with a complex mechanism of transcriptional autoregulation. Here, we show that the Xre-RES complex interacts specifically with a palindromic DNA repeat in the promoter in a 1:1 molar ratio, leading to transcriptional repression. We determine the 2.7 Å crystal structure of the protein-DNA complex, revealing an unexpected asymmetry in the interaction and suggesting the presence of a secondary binding site, which is supported by structural prediction of the binding to the intact promoter region. Additionally, we show that the antitoxin can be partially dislodged from the Xre-RES complex, resulting in Xre monomers and a 2:2 Xre-RES complex, neither of which repress transcription. These findings highlight a dynamic, concentration-dependent model of transcriptional autoregulation, in which the Xre-RES complex transitions between a non-binding (2:2) and a DNA-binding (4:2) form. |
| format | Article |
| id | doaj-art-dacef08bc05d4208a929256c423b63b5 |
| institution | Kabale University |
| issn | 1553-7390 1553-7404 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj-art-dacef08bc05d4208a929256c423b63b52025-08-23T05:31:37ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042025-06-01216e101174910.1371/journal.pgen.1011749Structural basis for higher-order DNA binding by a bacterial transcriptional regulator.Frederik Oskar Graversgaard HenriksenLan Bich VanDitlev Egeskov BrodersenRagnhild Bager SkjerningTranscriptional regulation by binding of transcription factors to palindromic sequences in promoter regions is a fundamental process in bacteria. Some transcription factors have multiple dimeric DNA-binding domains, in principle enabling interaction with higher-order DNA structures; however, mechanistic and structural insights into this phenomenon remain limited. The Pseudomonas putida toxin-antitoxin (TA) system Xre-RES has an unusual 4:2 stoichiometry including two potential DNA-binding sites, compatible with a complex mechanism of transcriptional autoregulation. Here, we show that the Xre-RES complex interacts specifically with a palindromic DNA repeat in the promoter in a 1:1 molar ratio, leading to transcriptional repression. We determine the 2.7 Å crystal structure of the protein-DNA complex, revealing an unexpected asymmetry in the interaction and suggesting the presence of a secondary binding site, which is supported by structural prediction of the binding to the intact promoter region. Additionally, we show that the antitoxin can be partially dislodged from the Xre-RES complex, resulting in Xre monomers and a 2:2 Xre-RES complex, neither of which repress transcription. These findings highlight a dynamic, concentration-dependent model of transcriptional autoregulation, in which the Xre-RES complex transitions between a non-binding (2:2) and a DNA-binding (4:2) form.https://doi.org/10.1371/journal.pgen.1011749 |
| spellingShingle | Frederik Oskar Graversgaard Henriksen Lan Bich Van Ditlev Egeskov Brodersen Ragnhild Bager Skjerning Structural basis for higher-order DNA binding by a bacterial transcriptional regulator. PLoS Genetics |
| title | Structural basis for higher-order DNA binding by a bacterial transcriptional regulator. |
| title_full | Structural basis for higher-order DNA binding by a bacterial transcriptional regulator. |
| title_fullStr | Structural basis for higher-order DNA binding by a bacterial transcriptional regulator. |
| title_full_unstemmed | Structural basis for higher-order DNA binding by a bacterial transcriptional regulator. |
| title_short | Structural basis for higher-order DNA binding by a bacterial transcriptional regulator. |
| title_sort | structural basis for higher order dna binding by a bacterial transcriptional regulator |
| url | https://doi.org/10.1371/journal.pgen.1011749 |
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