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DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in Sulfolobus acidocaldarius

In archaeal microorganisms, the compaction and organization of the chromosome into a dynamic but condensed structure is mediated by diverse chromatin-organizing proteins in a lineage-specific manner. While many archaea employ eukaryotic-type histones for nucleoid organization, this is not the case f...

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Autores principales: Lemmens, Liesbeth, Wang, Kun, Ruykens, Ebert, Nguyen, Van Tinh, Lindås, Ann-Christin, Willaert, Ronnie, Couturier, Mohea, Peeters, Eveline
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9025068/
https://www.ncbi.nlm.nih.gov/pubmed/35454113
http://dx.doi.org/10.3390/biom12040524
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author Lemmens, Liesbeth
Wang, Kun
Ruykens, Ebert
Nguyen, Van Tinh
Lindås, Ann-Christin
Willaert, Ronnie
Couturier, Mohea
Peeters, Eveline
author_facet Lemmens, Liesbeth
Wang, Kun
Ruykens, Ebert
Nguyen, Van Tinh
Lindås, Ann-Christin
Willaert, Ronnie
Couturier, Mohea
Peeters, Eveline
author_sort Lemmens, Liesbeth
collection PubMed
description In archaeal microorganisms, the compaction and organization of the chromosome into a dynamic but condensed structure is mediated by diverse chromatin-organizing proteins in a lineage-specific manner. While many archaea employ eukaryotic-type histones for nucleoid organization, this is not the case for the crenarchaeal model species Sulfolobus acidocaldarius and related species in Sulfolobales, in which the organization appears to be mostly reliant on the action of small basic DNA-binding proteins. There is still a lack of a full understanding of the involved proteins and their functioning. Here, a combination of in vitro and in vivo methodologies is used to study the DNA-binding properties of Sul12a, an uncharacterized small basic protein conserved in several Sulfolobales species displaying a winged helix–turn–helix structural motif and annotated as a transcription factor. Genome-wide chromatin immunoprecipitation and target-specific electrophoretic mobility shift assays demonstrate that Sul12a of S. acidocaldarius interacts with DNA in a non-sequence specific manner, while atomic force microscopy imaging of Sul12a–DNA complexes indicate that the protein induces structural effects on the DNA template. Based on these results, and a contrario to its initial annotation, it can be concluded that Sul12a is a novel chromatin-organizing protein.
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spelling pubmed-90250682022-04-23 DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in Sulfolobus acidocaldarius Lemmens, Liesbeth Wang, Kun Ruykens, Ebert Nguyen, Van Tinh Lindås, Ann-Christin Willaert, Ronnie Couturier, Mohea Peeters, Eveline Biomolecules Article In archaeal microorganisms, the compaction and organization of the chromosome into a dynamic but condensed structure is mediated by diverse chromatin-organizing proteins in a lineage-specific manner. While many archaea employ eukaryotic-type histones for nucleoid organization, this is not the case for the crenarchaeal model species Sulfolobus acidocaldarius and related species in Sulfolobales, in which the organization appears to be mostly reliant on the action of small basic DNA-binding proteins. There is still a lack of a full understanding of the involved proteins and their functioning. Here, a combination of in vitro and in vivo methodologies is used to study the DNA-binding properties of Sul12a, an uncharacterized small basic protein conserved in several Sulfolobales species displaying a winged helix–turn–helix structural motif and annotated as a transcription factor. Genome-wide chromatin immunoprecipitation and target-specific electrophoretic mobility shift assays demonstrate that Sul12a of S. acidocaldarius interacts with DNA in a non-sequence specific manner, while atomic force microscopy imaging of Sul12a–DNA complexes indicate that the protein induces structural effects on the DNA template. Based on these results, and a contrario to its initial annotation, it can be concluded that Sul12a is a novel chromatin-organizing protein. MDPI 2022-03-30 /pmc/articles/PMC9025068/ /pubmed/35454113 http://dx.doi.org/10.3390/biom12040524 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Lemmens, Liesbeth
Wang, Kun
Ruykens, Ebert
Nguyen, Van Tinh
Lindås, Ann-Christin
Willaert, Ronnie
Couturier, Mohea
Peeters, Eveline
DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in Sulfolobus acidocaldarius
title DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in Sulfolobus acidocaldarius
title_full DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in Sulfolobus acidocaldarius
title_fullStr DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in Sulfolobus acidocaldarius
title_full_unstemmed DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in Sulfolobus acidocaldarius
title_short DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in Sulfolobus acidocaldarius
title_sort dna-binding properties of a novel crenarchaeal chromatin-organizing protein in sulfolobus acidocaldarius
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9025068/
https://www.ncbi.nlm.nih.gov/pubmed/35454113
http://dx.doi.org/10.3390/biom12040524
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