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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...

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Autores principales: Erkelens, Amanda M., Henneman, Bram, van der Valk, Ramon A., Kirolos, Nancy C. S., Dame, Remus T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10151503/
https://www.ncbi.nlm.nih.gov/pubmed/37143534
http://dx.doi.org/10.3389/fmicb.2023.1166608
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author Erkelens, Amanda M.
Henneman, Bram
van der Valk, Ramon A.
Kirolos, Nancy C. S.
Dame, Remus T.
author_facet Erkelens, Amanda M.
Henneman, Bram
van der Valk, Ramon A.
Kirolos, Nancy C. S.
Dame, Remus T.
author_sort Erkelens, Amanda M.
collection PubMed
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.
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spelling pubmed-101515032023-05-03 Specific DNA binding of archaeal histones HMfA and HMfB Erkelens, Amanda M. Henneman, Bram van der Valk, Ramon A. Kirolos, Nancy C. S. Dame, Remus T. Front Microbiol Microbiology 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. Frontiers Media S.A. 2023-04-18 /pmc/articles/PMC10151503/ /pubmed/37143534 http://dx.doi.org/10.3389/fmicb.2023.1166608 Text en Copyright © 2023 Erkelens, Henneman, van der Valk, Kirolos and Dame. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Erkelens, Amanda M.
Henneman, Bram
van der Valk, Ramon A.
Kirolos, Nancy C. S.
Dame, Remus T.
Specific DNA binding of archaeal histones HMfA and HMfB
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 Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10151503/
https://www.ncbi.nlm.nih.gov/pubmed/37143534
http://dx.doi.org/10.3389/fmicb.2023.1166608
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