DNA sequence-directed cooperation between nucleoid-associated proteins

Japaridze, A.; Yang, W.W.W.; Dekker, C.; Nasser, William; Muskhelishvili, Georgi

doi:10.1016/j.isci.2021.102408

DNA sequence-directed cooperation between nucleoid-associated proteins

Title

DNA sequence-directed cooperation between nucleoid-associated proteins

Author

Japaridze, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)
Yang, W.W.W. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)
Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)
Nasser, William (INSA Lyon)
Muskhelishvili, Georgi (Agricultural University of Georgia, Tbilisi)

Date

2021

Abstract

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.

Subject

Organizational Aspects of Cell Biology
Structural Biology

To reference this document use:

http://resolver.tudelft.nl/uuid:c24d9ed0-c9e9-4e87-bf44-c2815a468950

DOI

https://doi.org/10.1016/j.isci.2021.102408

ISSN

2589-0042

Source

iScience, 24 (5)

Part of collection

Institutional Repository