title: The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction.
abstract: BACKGROUND
  The Escherichia coli heterodimeric HU protein is a small DNA-bending protein associated with the bacterial nucleoid. It can introduce negative supercoils into closed circular DNA in the presence of topoisomerase I. Cells lacking HU grow very poorly and display many phenotypes.
  
  
  RESULTS
  We analyzed the transcription profile of every Escherichia coli gene in the absence of one or both HU subunits. This genome-wide in silico transcriptomic approach, performed in parallel with in vivo genetic experimentation, defined the HU regulon. This large regulon, which comprises 8% of the genome, is composed of four biologically relevant gene classes whose regulation responds to anaerobiosis, acid stress, high osmolarity, and SOS induction.
  
  
  CONCLUSIONS
  The regulation a large number of genes encoding enzymes involved in energy metabolism and catabolism pathways by HU explains the highly pleiotropic phenotype of HU-deficient cells. The uniform chromosomal distribution of the many operons regulated by HU strongly suggests that the transcriptional and nucleoid architectural functions of HU constitute two aspects of a unique protein-DNA interaction mechanism.
authors.affiliation: Laboratoire de Physiologie Bactérienne, CNRS, UPR 9073, Institut de Biologie Physico-Chimique, Paris, France. jacques.oberto@igmors.u-psud.fr
authors.forename: Jacques
authors.initials: J
authors.lastname: Oberto
authors.forename: Sabrina
authors.initials: S
authors.lastname: Nabti
authors.forename: Valérie
authors.initials: V
authors.lastname: Jooste
authors.forename: Hervé
authors.initials: H
authors.lastname: Mignot
authors.forename: Josette
authors.initials: J
authors.lastname: Rouviere-Yaniv
mesh_terms: D000143:Acids; D000332:Aerobiosis / Q000235:genetics; D000693:Anaerobiosis / Q000235:genetics; D016000:Cluster Analysis; D004278:DNA, Superhelical / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics*; D030541:Databases, Genetic; D004734:Energy Metabolism / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D007700:Kinetics; D007763:Lac Operon; D020411:Oligonucleotide Array Sequence Analysis; D009994:Osmolar Concentration; D010641:Phenotype; D018085:Regulon / Q000235:genetics*; D015203:Reproducibility of Results; D013014:SOS Response, Genetics / Q000235:genetics*; D013312:Stress, Physiological / Q000235:genetics*; D014158:Transcription, Genetic; D001616:beta-Galactosidase / Q000378:metabolism
chemical_list: D000143:Acids; D004278:DNA, Superhelical; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C116822:hns protein, E coli; D001616:beta-Galactosidase