ATP-independent Cooperative Binding of Yeast Isw1a to Bare and Nucleosomal DNA

PLoS One. 2012;7(2):e31845. doi: 10.1371/journal.pone.0031845. Epub 2012 Feb 16.

Abstract

Among chromatin remodeling factors, the ISWI family displays a nucleosome-enhanced ATPase activity coupled to DNA translocation. While these enzymes are known to bind to DNA, their activity has not been fully characterized. Here we use TEM imaging and single molecule manipulation to investigate the interaction between DNA and yeast Isw1a. We show that Isw1a displays a highly cooperative ATP-independent binding to and bridging between DNA segments. Under appropriate tension, rare single nucleation events can sometimes be observed and loop DNA with a regular step. These nucleation events are often followed by binding of successive complexes bridging between nearby DNA segments in a zipper-like fashion, as confirmed by TEM observations. On nucleosomal substrates, we show that the specific ATP-dependent remodeling activity occurs in the context of cooperative Isw1a complexes bridging extranucleosomal DNA. Our results are interpreted in the context of the recently published partial structure of Isw1a and support its acting as a "protein ruler" (with possibly more than one tick).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases / metabolism*
  • Adenosine Triphosphatases / ultrastructure
  • Adenosine Triphosphate / metabolism
  • DNA, Fungal / metabolism*
  • DNA, Fungal / ultrastructure
  • DNA-Binding Proteins / metabolism*
  • DNA-Binding Proteins / ultrastructure
  • Microscopy, Electron, Transmission
  • Nucleosomes / metabolism*
  • Protein Binding
  • Saccharomyces cerevisiae / enzymology*
  • Saccharomyces cerevisiae / ultrastructure
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Saccharomyces cerevisiae Proteins / ultrastructure
  • Substrate Specificity

Substances

  • DNA, Fungal
  • DNA-Binding Proteins
  • Nucleosomes
  • Saccharomyces cerevisiae Proteins
  • Adenosine Triphosphate
  • Adenosine Triphosphatases
  • ISW1 protein, S cerevisiae