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DNA sequence-directed cooperation between nucleoid-associated proteins

Nucleoid-associated proteins (NAPs) are a class of highly abundant DNA-binding proteins in bacteria and archaea. While both the composition and relative abundance of the NAPs change during the bacterial growth cycle, surprisingly little is known about their crosstalk in mutually binding and stabiliz...

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Autores principales: Japaridze, Aleksandre, Yang, Wayne, Dekker, Cees, Nasser, William, Muskhelishvili, Georgi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8099737/
https://www.ncbi.nlm.nih.gov/pubmed/33997690
http://dx.doi.org/10.1016/j.isci.2021.102408
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author Japaridze, Aleksandre
Yang, Wayne
Dekker, Cees
Nasser, William
Muskhelishvili, Georgi
author_facet Japaridze, Aleksandre
Yang, Wayne
Dekker, Cees
Nasser, William
Muskhelishvili, Georgi
author_sort Japaridze, Aleksandre
collection PubMed
description Nucleoid-associated proteins (NAPs) are a class of highly abundant DNA-binding proteins in bacteria and archaea. While both the composition and relative abundance of the NAPs change during the bacterial growth cycle, surprisingly little is known about their crosstalk in mutually binding and stabilizing higher-order nucleoprotein complexes in the bacterial chromosome. Here, we use atomic force microscopy and solid-state nanopores to investigate long-range nucleoprotein structures formed by the binding of two major NAPs, FIS and H-NS, to DNA molecules with distinct binding site arrangements. We find that spatial organization of the protein binding sites can govern the higher-order architecture of the nucleoprotein complexes. Based on sequence arrangement the complexes differed in their global shape and compaction as well as the extent of FIS and H-NS binding. Our observations highlight the important role the DNA sequence plays in driving structural differentiation within the bacterial chromosome.
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spelling pubmed-80997372021-05-13 DNA sequence-directed cooperation between nucleoid-associated proteins Japaridze, Aleksandre Yang, Wayne Dekker, Cees Nasser, William Muskhelishvili, Georgi iScience Article Nucleoid-associated proteins (NAPs) are a class of highly abundant DNA-binding proteins in bacteria and archaea. While both the composition and relative abundance of the NAPs change during the bacterial growth cycle, surprisingly little is known about their crosstalk in mutually binding and stabilizing higher-order nucleoprotein complexes in the bacterial chromosome. Here, we use atomic force microscopy and solid-state nanopores to investigate long-range nucleoprotein structures formed by the binding of two major NAPs, FIS and H-NS, to DNA molecules with distinct binding site arrangements. We find that spatial organization of the protein binding sites can govern the higher-order architecture of the nucleoprotein complexes. Based on sequence arrangement the complexes differed in their global shape and compaction as well as the extent of FIS and H-NS binding. Our observations highlight the important role the DNA sequence plays in driving structural differentiation within the bacterial chromosome. Elsevier 2021-04-20 /pmc/articles/PMC8099737/ /pubmed/33997690 http://dx.doi.org/10.1016/j.isci.2021.102408 Text en © 2021 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Article
Japaridze, Aleksandre
Yang, Wayne
Dekker, Cees
Nasser, William
Muskhelishvili, Georgi
DNA sequence-directed cooperation between nucleoid-associated proteins
title DNA sequence-directed cooperation between nucleoid-associated proteins
title_full DNA sequence-directed cooperation between nucleoid-associated proteins
title_fullStr DNA sequence-directed cooperation between nucleoid-associated proteins
title_full_unstemmed DNA sequence-directed cooperation between nucleoid-associated proteins
title_short DNA sequence-directed cooperation between nucleoid-associated proteins
title_sort dna sequence-directed cooperation between nucleoid-associated proteins
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8099737/
https://www.ncbi.nlm.nih.gov/pubmed/33997690
http://dx.doi.org/10.1016/j.isci.2021.102408
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