DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in <i>Sulfolobus acidocaldarius</i>
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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| Format: | Article |
| Language: | English |
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MDPI AG
2022-03-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/12/4/524 |
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| author | Liesbeth Lemmens Kun Wang Ebert Ruykens Van Tinh Nguyen Ann-Christin Lindås Ronnie Willaert Mohea Couturier Eveline Peeters |
| author_facet | Liesbeth Lemmens Kun Wang Ebert Ruykens Van Tinh Nguyen Ann-Christin Lindås Ronnie Willaert Mohea Couturier Eveline Peeters |
| author_sort | Liesbeth Lemmens |
| collection | DOAJ |
| 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 <i>Sulfolobus acidocaldarius</i> 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 <i>S. acidocaldarius</i> 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 <i>a contrario</i> to its initial annotation, it can be concluded that Sul12a is a novel chromatin-organizing protein. |
| first_indexed | 2024-03-09T11:05:56Z |
| format | Article |
| id | doaj.art-3031dd79a29f426db645bcf0bdc14e77 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-09T11:05:56Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-3031dd79a29f426db645bcf0bdc14e772023-12-01T00:55:48ZengMDPI AGBiomolecules2218-273X2022-03-0112452410.3390/biom12040524DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in <i>Sulfolobus acidocaldarius</i>Liesbeth Lemmens0Kun Wang1Ebert Ruykens2Van Tinh Nguyen3Ann-Christin Lindås4Ronnie Willaert5Mohea Couturier6Eveline Peeters7Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, B-1050 Brussels, BelgiumDepartment of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 11597 Stockholm, SwedenResearch Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, B-1050 Brussels, BelgiumResearch Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, B-1050 Brussels, BelgiumDepartment of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 11597 Stockholm, SwedenResearch Group Structural Biology Brussels, Alliance Research Group VUB-UGent NanoMicrobiology, International Joint Research Group VUB-EFPL NanoBiotechnology & NanoMedicine, Department of Bioengineering Sciences, Vrije Universiteit Brussel, B-1050 Brussels, BelgiumResearch Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, B-1050 Brussels, BelgiumResearch Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, B-1050 Brussels, BelgiumIn 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 <i>Sulfolobus acidocaldarius</i> 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 <i>S. acidocaldarius</i> 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 <i>a contrario</i> to its initial annotation, it can be concluded that Sul12a is a novel chromatin-organizing protein.https://www.mdpi.com/2218-273X/12/4/524archaea<i>Sulfolobus</i>nucleoid-associated proteinDNA bindingatomic force microscopychromatin structure |
| spellingShingle | Liesbeth Lemmens Kun Wang Ebert Ruykens Van Tinh Nguyen Ann-Christin Lindås Ronnie Willaert Mohea Couturier Eveline Peeters DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in <i>Sulfolobus acidocaldarius</i> Biomolecules archaea <i>Sulfolobus</i> nucleoid-associated protein DNA binding atomic force microscopy chromatin structure |
| title | DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in <i>Sulfolobus acidocaldarius</i> |
| title_full | DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in <i>Sulfolobus acidocaldarius</i> |
| title_fullStr | DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in <i>Sulfolobus acidocaldarius</i> |
| title_full_unstemmed | DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in <i>Sulfolobus acidocaldarius</i> |
| title_short | DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in <i>Sulfolobus acidocaldarius</i> |
| title_sort | dna binding properties of a novel crenarchaeal chromatin organizing protein in i sulfolobus acidocaldarius i |
| topic | archaea <i>Sulfolobus</i> nucleoid-associated protein DNA binding atomic force microscopy chromatin structure |
| url | https://www.mdpi.com/2218-273X/12/4/524 |
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