Physical organization of DNA by multiple non-specific DNA-binding modes of integration host factor (IHF)
The integration host factor (IHF) is an abundant nucleoid-associated protein and an essential co-factor for phage λ site-specific recombination and gene regulation in E. coli. Introduction of a sharp DNA kink at specific cognate sites is critical for these functions. Interestingly, the intracellular...
| Main Authors: | , , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2013
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/95346 http://hdl.handle.net/10220/9317 |
| _version_ | 1826116552153366528 |
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| author | Lin, Jie Chen, Hu Dröge, Peter Yan, Jie |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Lin, Jie Chen, Hu Dröge, Peter Yan, Jie |
| author_sort | Lin, Jie |
| collection | NTU |
| description | The integration host factor (IHF) is an abundant nucleoid-associated protein and an essential co-factor for phage λ site-specific recombination and gene regulation in E. coli. Introduction of a sharp DNA kink at specific cognate sites is critical for these functions. Interestingly, the intracellular concentration of IHF is much higher than the concentration needed for site-specific interactions, suggesting that non-specific binding of IHF to DNA plays a role in the physical organization of bacterial chromatin. However, it is unclear how non-specific DNA association contributes to DNA organization. By using a combination of single DNA manipulation and atomic force microscopy imaging methods, we show here that distinct modes of non-specific DNA binding of IHF result in complex global DNA conformations. Changes in KCl and IHF concentrations, as well as tension applied to DNA, dramatically influence the degree of DNA-bending. In addition, IHF can crosslink DNA into a highly compact DNA meshwork that is observed in the presence of magnesium at low concentration of monovalent ions and high IHF-DNA stoichiometries. Our findings provide important insights into how IHF contributes to bacterial chromatin organization, gene regulation, and biofilm formation. |
| first_indexed | 2024-10-01T04:13:34Z |
| format | Journal Article |
| id | ntu-10356/95346 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T04:13:34Z |
| publishDate | 2013 |
| record_format | dspace |
| spelling | ntu-10356/953462023-02-28T17:01:37Z Physical organization of DNA by multiple non-specific DNA-binding modes of integration host factor (IHF) Lin, Jie Chen, Hu Dröge, Peter Yan, Jie School of Biological Sciences DRNTU::Science::Biological sciences::Genetics The integration host factor (IHF) is an abundant nucleoid-associated protein and an essential co-factor for phage λ site-specific recombination and gene regulation in E. coli. Introduction of a sharp DNA kink at specific cognate sites is critical for these functions. Interestingly, the intracellular concentration of IHF is much higher than the concentration needed for site-specific interactions, suggesting that non-specific binding of IHF to DNA plays a role in the physical organization of bacterial chromatin. However, it is unclear how non-specific DNA association contributes to DNA organization. By using a combination of single DNA manipulation and atomic force microscopy imaging methods, we show here that distinct modes of non-specific DNA binding of IHF result in complex global DNA conformations. Changes in KCl and IHF concentrations, as well as tension applied to DNA, dramatically influence the degree of DNA-bending. In addition, IHF can crosslink DNA into a highly compact DNA meshwork that is observed in the presence of magnesium at low concentration of monovalent ions and high IHF-DNA stoichiometries. Our findings provide important insights into how IHF contributes to bacterial chromatin organization, gene regulation, and biofilm formation. Published version 2013-03-01T02:26:41Z 2019-12-06T19:13:06Z 2013-03-01T02:26:41Z 2019-12-06T19:13:06Z 2012 2012 Journal Article Lin, J., Chen, H., Dröge, P., & Yan, J. (2012). Physical Organization of DNA by Multiple Non-Specific DNA-Binding Modes of Integration Host Factor (IHF). PLoS ONE, 7(11), e49885. 1932-6203 https://hdl.handle.net/10356/95346 http://hdl.handle.net/10220/9317 10.1371/journal.pone.0049885 23166787 en PLoS ONE © 2012 The Authors. application/pdf |
| spellingShingle | DRNTU::Science::Biological sciences::Genetics Lin, Jie Chen, Hu Dröge, Peter Yan, Jie Physical organization of DNA by multiple non-specific DNA-binding modes of integration host factor (IHF) |
| title | Physical organization of DNA by multiple non-specific DNA-binding modes of integration host factor (IHF) |
| title_full | Physical organization of DNA by multiple non-specific DNA-binding modes of integration host factor (IHF) |
| title_fullStr | Physical organization of DNA by multiple non-specific DNA-binding modes of integration host factor (IHF) |
| title_full_unstemmed | Physical organization of DNA by multiple non-specific DNA-binding modes of integration host factor (IHF) |
| title_short | Physical organization of DNA by multiple non-specific DNA-binding modes of integration host factor (IHF) |
| title_sort | physical organization of dna by multiple non specific dna binding modes of integration host factor ihf |
| topic | DRNTU::Science::Biological sciences::Genetics |
| url | https://hdl.handle.net/10356/95346 http://hdl.handle.net/10220/9317 |
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