Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein.
Structural differentiation of bacterial chromatin depends on cooperative binding of abundant nucleoid-associated proteins at numerous genomic DNA sites and stabilization of distinct long-range nucleoprotein structures. Histone-like nucleoid-structuring protein (H-NS) is an abundant DNA-bridging, nucleoid-associated protein that binds to an AT-rich conserved DNA sequence motif and regulates both the shape and the genetic expression of the bacterial chromosome. Although there is ample evidence that the mode of H-NS binding depends on environmental conditions, the role of the spatial organization of H-NS-binding sequences in the assembly of long-range nucleoprotein structures remains unknown. In this study, by using high-resolution atomic force microscopy combined with biochemical assays, we explored the formation of H-NS nucleoprotein complexes on circular DNA molecules having different arrangements of identical sequences containing high-affinity H-NS-binding sites. We provide the first experimental evidence that variable sequence arrangements result in various three-dimensional nucleoprotein structures that differ in their shape and the capacity to constrain supercoils and compact the DNA. We believe that the DNA sequence-directed versatile assembly of periodic higher-order structures reveals a general organizational principle that can be exploited for knowledge-based design of long-range nucleoprotein complexes and purposeful manipulation of the bacterial chromatin architecture.
From the Laboratory of Physics of Living Matter, EPFL (École Polytechnique Fédérale de Lausanne), CE 3 316 Lausanne, Switzerland.
Aleksandre
A
Japaridze
From the Laboratory of Physics of Living Matter, EPFL (École Polytechnique Fédérale de Lausanne), CE 3 316 Lausanne, Switzerland.
Sylvain
S
Renevey
Jacobs University, D-28759 Bremen, Germany.
Patrick
P
Sobetzko
Jacobs University, D-28759 Bremen, Germany.
Liubov
L
Stoliar
UMR5240 CNRS/INSA/UCB, Université de Lyon, F-69003 INSA Lyon, Villeurbanne F-69621, France, and.
William
W
Nasser
From the Laboratory of Physics of Living Matter, EPFL (École Polytechnique Fédérale de Lausanne), CE 3 316 Lausanne, Switzerland, giovanni.dietler@epfl.ch.
Giovanni
G
Dietler
Jacobs University, D-28759 Bremen, Germany, g.muskhelishvili@jacobs-university.de.|Agricultural University of Georgia, 240 David Aghmashenebeli Alley, 0159 Tbilisi, Republik of Georgia.
Georgi
G
Muskhelishvili
D002843:Chromatin / Q000737:chemistry*; D004269:DNA, Bacterial / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D004926:Escherichia coli / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000737:chemistry*
D002843:Chromatin; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins
DNA binding protein; DNA binding sites; DNA topology; atomic force microscopy (AFM); bacterial chromatin; bacterial genetics; nucleoid-associated protein H-NS; nucleoprotein filaments; protein-DNA interaction