Specific DNA binding of archaeal histones HMfA and HMfB
In archaea, histones play a role in genome compaction and are involved in transcription regulation. Whereas archaeal histones bind DNA without sequence specificity, they bind preferentially to DNA containing repeats of alternating A/T and G/C motifs. These motifs are also present on the artificial s...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-04-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1166608/full |
| _version_ | 1827965334724804608 |
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| author | Amanda M. Erkelens Bram Henneman Ramon A. van der Valk Nancy C. S. Kirolos Remus T. Dame Remus T. Dame |
| author_facet | Amanda M. Erkelens Bram Henneman Ramon A. van der Valk Nancy C. S. Kirolos Remus T. Dame Remus T. Dame |
| author_sort | Amanda M. Erkelens |
| collection | DOAJ |
| description | In archaea, histones play a role in genome compaction and are involved in transcription regulation. Whereas archaeal histones bind DNA without sequence specificity, they bind preferentially to DNA containing repeats of alternating A/T and G/C motifs. These motifs are also present on the artificial sequence “Clone20,” a high-affinity model sequence for binding of the histones from Methanothermus fervidus. Here, we investigate the binding of HMfA and HMfB to Clone20 DNA. We show that specific binding at low protein concentrations (<30 nM) yields a modest level of DNA compaction, attributed to tetrameric nucleosome formation, whereas nonspecific binding strongly compacts DNA. We also demonstrate that histones impaired in hypernucleosome formation are still able to recognize the Clone20 sequence. Histone tetramers indeed exhibit a higher binding affinity for Clone20 than nonspecific DNA. Our results indicate that a high-affinity DNA sequence does not act as a nucleation site, but is bound by a tetramer which we propose is geometrically different from the hypernucleosome. Such a mode of histone binding might permit sequence-driven modulation of hypernucleosome size. These findings might be extrapolated to histone variants that do not form hypernucleosomes. Versatile binding modes of histones could provide a platform for functional interplay between genome compaction and transcription. |
| first_indexed | 2024-04-09T17:31:23Z |
| format | Article |
| id | doaj.art-5b0b41d6b1564249a77384b1633019b8 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-09T17:31:23Z |
| publishDate | 2023-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-5b0b41d6b1564249a77384b1633019b82023-04-18T04:17:59ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-04-011410.3389/fmicb.2023.11666081166608Specific DNA binding of archaeal histones HMfA and HMfBAmanda M. Erkelens0Bram Henneman1Ramon A. van der Valk2Nancy C. S. Kirolos3Remus T. Dame4Remus T. Dame5Leiden Institute of Chemistry, Leiden University, Leiden, NetherlandsLeiden Institute of Chemistry, Leiden University, Leiden, NetherlandsLeiden Institute of Chemistry, Leiden University, Leiden, NetherlandsLeiden Institute of Chemistry, Leiden University, Leiden, NetherlandsLeiden Institute of Chemistry, Leiden University, Leiden, NetherlandsCentre for Microbial Cell Biology, Leiden University, Leiden, NetherlandsIn archaea, histones play a role in genome compaction and are involved in transcription regulation. Whereas archaeal histones bind DNA without sequence specificity, they bind preferentially to DNA containing repeats of alternating A/T and G/C motifs. These motifs are also present on the artificial sequence “Clone20,” a high-affinity model sequence for binding of the histones from Methanothermus fervidus. Here, we investigate the binding of HMfA and HMfB to Clone20 DNA. We show that specific binding at low protein concentrations (<30 nM) yields a modest level of DNA compaction, attributed to tetrameric nucleosome formation, whereas nonspecific binding strongly compacts DNA. We also demonstrate that histones impaired in hypernucleosome formation are still able to recognize the Clone20 sequence. Histone tetramers indeed exhibit a higher binding affinity for Clone20 than nonspecific DNA. Our results indicate that a high-affinity DNA sequence does not act as a nucleation site, but is bound by a tetramer which we propose is geometrically different from the hypernucleosome. Such a mode of histone binding might permit sequence-driven modulation of hypernucleosome size. These findings might be extrapolated to histone variants that do not form hypernucleosomes. Versatile binding modes of histones could provide a platform for functional interplay between genome compaction and transcription.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1166608/fullHMfAHMfBhypernucleosomehigh-affinity DNA sequencearchaeal chromatinarchaeal nucleosome |
| spellingShingle | Amanda M. Erkelens Bram Henneman Ramon A. van der Valk Nancy C. S. Kirolos Remus T. Dame Remus T. Dame Specific DNA binding of archaeal histones HMfA and HMfB Frontiers in Microbiology HMfA HMfB hypernucleosome high-affinity DNA sequence archaeal chromatin archaeal nucleosome |
| title | Specific DNA binding of archaeal histones HMfA and HMfB |
| title_full | Specific DNA binding of archaeal histones HMfA and HMfB |
| title_fullStr | Specific DNA binding of archaeal histones HMfA and HMfB |
| title_full_unstemmed | Specific DNA binding of archaeal histones HMfA and HMfB |
| title_short | Specific DNA binding of archaeal histones HMfA and HMfB |
| title_sort | specific dna binding of archaeal histones hmfa and hmfb |
| topic | HMfA HMfB hypernucleosome high-affinity DNA sequence archaeal chromatin archaeal nucleosome |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1166608/full |
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