We are investigating the structure of E. coli chromosome and the pathway of its compaction to the nucleoid state by taking several approaches: (i) by genetically analyzing mutant cells defective in the nucleoid protein HU; (ii) by studying nuclease digestion patterns of E. coli nucleoids; (iii) by analyzing the chromosomal DNA sequence for the existence of potential ?structural codes?; and (iv) by determining the X-ray structure of the HU protein. We report here an E. coli mutant with an altered HU protein and the X-ray structure of the latter.

We isolated an E. coli mutant with an altered HU, which induces an intense nucleoid compaction in cell. The chromosomal condensation was accompanied by dramatic changes in the morphology, physiology, and metabolic profile including repression of many housekeeping genes involved in carbon catabolism and amino acid anabolism, but activation of quiescent genes associated with virulence in mammalian hosts. In vitro, purified mutant HU, unlike the wild-type protein, generated highly condensed, globular DNA-protein complexes upon interaction with free DNA, suggesting it is through reorganization of the nucleoid confirmation that the mutant HU sets the transcription pattern of a commensal E. coli towards a more pathogenic lifestyle.

We also determined the structure of E. coli HU by X-ray crystallography. The basic folds of the E. coli HU dimer are the same as found in previously determined structures of HU from other bacteria. However, we discovered that HU multimerizes to a repeating stacked octamer-unit, which would allow DNA to continuously wrap around the oligomeric protein using the exposed DNA-binding β arms. Such a nucleosome-like structure together with the observed phenotype of the HU mutant leads us to propose that the E. coli nucleoid architecture dictates the global transcription profile and, consequently, the overall bacterial behavioral pattern.