Gene clusters reflecting macrodomain structure respond to nucleoid perturbations

Mol Biosyst. 2011 Mar;7(3):878-88. doi: 10.1039/c0mb00213e. Epub 2010 Dec 16.


Focusing on the DNA-bridging nucleoid proteins Fis and H-NS, and integrating several independent experimental and bioinformatic data sources, we investigate the links between chromosomal spatial organization and global transcriptional regulation. By means of a novel multi-scale spatial aggregation analysis, we uncover the existence of contiguous clusters of nucleoid-perturbation sensitive genes along the genome, whose expression is affected by a combination of topological DNA state and nucleoid-shaping protein occupancy. The clusters correlate well with the macrodomain structure of the genome. The most significant of them lay symmetrically at the edges of the Ter macrodomain and involve all of the flagellar and chemotaxis machinery, in addition to key regulators of biofilm formation, suggesting that the regulation of the physical state of the chromosome by the nucleoid proteins plays an important role in coordinating the transcriptional response leading to the switch between a motile and a biofilm lifestyle.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Biofilms / growth & development
  • DNA, Bacterial / chemistry*
  • DNA, Bacterial / genetics*
  • DNA, Superhelical / chemistry
  • DNA, Superhelical / genetics
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Factor For Inversion Stimulation Protein / chemistry
  • Factor For Inversion Stimulation Protein / genetics
  • Factor For Inversion Stimulation Protein / metabolism
  • Gene Deletion
  • Genome, Bacterial / genetics
  • Multigene Family / genetics*
  • Nucleic Acid Conformation
  • Oligonucleotide Array Sequence Analysis
  • Protein Conformation
  • Transcription, Genetic / genetics


  • Bacterial Proteins
  • DNA, Bacterial
  • DNA, Superhelical
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • Factor For Inversion Stimulation Protein
  • Fis protein, E coli
  • H-NS protein, bacteria