A systematic in vitro study of nucleoprotein complexes formed by bacterial nucleoid-associated proteins revealing novel types of DNA organization

J Mol Biol. 2009 Apr 17;387(5):1261-76. doi: 10.1016/j.jmb.2009.02.050. Epub 2009 Feb 28.

Abstract

Bacterial nucleoid is a dynamic entity that changes its three-dimensional shape and compaction depending on cellular physiology. While these changes are tightly associated with compositional alterations of abundant nucleoid-associated proteins implicated in reshaping the nucleoid, their cooperation in regular long-range DNA organization is poorly understood. In this study, we reconstitute a novel nucleoprotein structure in vitro, which is stabilized by cooperative effects of major bacterial DNA architectural proteins. While, individually, these proteins stabilize alternative DNA architectures consistent with either plectonemic or toroidal coiling of DNA, the combination of histone-like protein, histone-like nucleoid structuring protein, and integration host factor produces a conspicuous semiperiodic structure. By employing a bottom-up in vitro approach, we thus characterize a minimum set of bacterial proteins cooperating in organizing a regular DNA structure. Visualized structures suggest a mechanism for nucleation of topological transitions underlying the reshaping of DNA by bacterial nucleoid-associated proteins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / ultrastructure
  • Bacteriophage lambda / chemistry
  • Chromatin / chemistry
  • DNA, Viral / chemistry
  • DNA, Viral / ultrastructure
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / ultrastructure
  • Integration Host Factors / chemistry
  • Integration Host Factors / genetics
  • Integration Host Factors / ultrastructure
  • Macromolecular Substances / chemistry
  • Microscopy, Atomic Force
  • Models, Genetic
  • Models, Molecular
  • Nucleic Acid Conformation
  • Nucleoproteins / chemistry*
  • Nucleoproteins / genetics
  • Nucleoproteins / ultrastructure

Substances

  • Bacterial Proteins
  • Chromatin
  • DNA, Viral
  • DNA-Binding Proteins
  • H-NS protein, bacteria
  • Integration Host Factors
  • Macromolecular Substances
  • Nucleoproteins
  • histone-like protein HU, bacteria