TY - JOUR
T1 - DNA sequence-directed cooperation between nucleoid-associated proteins
AU - Japaridze, Aleksandre
AU - Yang, Wayne
AU - Dekker, Cees
AU - Nasser, William
AU - Muskhelishvili, Georgi
PY - 2021
Y1 - 2021
N2 - 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.
AB - 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.
KW - Organizational Aspects of Cell Biology
KW - Structural Biology
UR - http://www.scopus.com/inward/record.url?scp=85104678114&partnerID=8YFLogxK
U2 - 10.1016/j.isci.2021.102408
DO - 10.1016/j.isci.2021.102408
M3 - Article
AN - SCOPUS:85104678114
SN - 2589-0042
VL - 24
JO - iScience
JF - iScience
IS - 5
M1 - 102408
ER -